######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Ancylostoma ceylanicum/A. ceylanicum - ancCey1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzAncCey1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzAncCey1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs ancCey1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Ancylostoma ceylanicum/A. ceylanicum - ancCey1 SEQ2_DIR=/hive/data/genomes/ancCey1/ancCey1.2bit SEQ2_LEN=/hive/data/genomes/ancCey1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzAncCey1.2015-08-16 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 5m15.102s cat fb.hetBac1.chainAncCey1Link.txt # 17478863 bases of 74374900 (23.501%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 ancCey1) > rbest.log 2>&1 & # real 0m52.365s # and for the swap: mkdir /hive/data/genomes/ancCey1/bed/blastz.hetBac1.swap cd /hive/data/genomes/ancCey1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzAncCey1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 4m54.136s cat fb.ancCey1.chainHetBac1Link.txt # 18606453 bases of 300914990 (6.183%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ancCey1 hetBac1) \ > rbest.log 2>&1 # real 2m25.085s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Ascaris suum/Pig roundworm - ascSuu1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzAscSuu1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzAscSuu1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs ascSuu1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Ascaris suum/Pig roundworm - ascSuu1 SEQ2_DIR=/hive/data/genomes/ascSuu1/ascSuu1.2bit SEQ2_LEN=/hive/data/genomes/ascSuu1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzAscSuu1.2015-08-16 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 5m4.260s cat fb.hetBac1.chainAscSuu1Link.txt # 6541366 bases of 74374900 (8.795%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 ascSuu1) > rbest.log 2>&1 & # real 0m30.047s # and for the swap: mkdir /hive/data/genomes/ascSuu1/bed/blastz.hetBac1.swap cd /hive/data/genomes/ascSuu1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzAscSuu1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m4.840s cat fb.ascSuu1.chainHetBac1Link.txt # 6742130 bases of 262604320 (2.567%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` ascSuu1 hetBac1) \ > rbest.log 2>&1 # real 0m42.597s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Brugia malayi/Filarial worm - bruMal2 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzBruMal2.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzBruMal2.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs bruMal2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Brugia malayi/Filarial worm - bruMal2 SEQ2_DIR=/hive/data/genomes/bruMal2/bruMal2.2bit SEQ2_LEN=/hive/data/genomes/bruMal2/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzBruMal2.2015-08-16 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 3m23.348s cat fb.hetBac1.chainBruMal2Link.txt # 7027176 bases of 74374900 (9.448%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 bruMal2) > rbest.log 2>&1 & # real 0m30.399s # and for the swap: mkdir /hive/data/genomes/bruMal2/bed/blastz.hetBac1.swap cd /hive/data/genomes/bruMal2/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzBruMal2.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m41.374s cat fb.bruMal2.chainHetBac1Link.txt # 7231658 bases of 87424120 (8.272%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` bruMal2 hetBac1) \ > rbest.log 2>&1 # real 0m37.614s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Bursaphelenchus xylophilus/Pine wood nematode - burXyl1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzBurXyl1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzBurXyl1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs burXyl1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Bursaphelenchus xylophilus/Pine wood nematode - burXyl1 SEQ2_DIR=/hive/data/genomes/burXyl1/burXyl1.2bit SEQ2_LEN=/hive/data/genomes/burXyl1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzBurXyl1.2015-08-16 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 3m16.402s cat fb.hetBac1.chainBurXyl1Link.txt # 5460333 bases of 74374900 (7.342%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 burXyl1) > rbest.log 2>&1 & # real 0m27.211s # and for the swap: mkdir /hive/data/genomes/burXyl1/bed/blastz.hetBac1.swap cd /hive/data/genomes/burXyl1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzBurXyl1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m50.462s cat fb.burXyl1.chainHetBac1Link.txt # 5176771 bases of 73100506 (7.082%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` burXyl1 hetBac1) \ > rbest.log 2>&1 # real 0m31.927s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Dirofilaria immitis/Dog heartworm - dirImm1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzDirImm1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzDirImm1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs dirImm1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Dirofilaria immitis/Dog heartworm - dirImm1 SEQ2_DIR=/hive/data/genomes/dirImm1/dirImm1.2bit SEQ2_LEN=/hive/data/genomes/dirImm1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzDirImm1.2015-08-16 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 4m36.689s cat fb.hetBac1.chainDirImm1Link.txt # 6873603 bases of 74374900 (9.242%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 dirImm1) > rbest.log 2>&1 & # real 0m29.743s # and for the swap: mkdir /hive/data/genomes/dirImm1/bed/blastz.hetBac1.swap cd /hive/data/genomes/dirImm1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzDirImm1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m18.594s cat fb.dirImm1.chainHetBac1Link.txt # 6778403 bases of 84923352 (7.982%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` dirImm1 hetBac1) \ > rbest.log 2>&1 # real 1m24.556s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Haemonchus contortus/Barber pole worm - haeCon2 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzHaeCon2.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzHaeCon2.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs haeCon2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Haemonchus contortus/Barber pole worm - haeCon2 SEQ2_DIR=/hive/data/genomes/haeCon2/haeCon2.2bit SEQ2_LEN=/hive/data/genomes/haeCon2/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzHaeCon2.2015-08-16 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 4m48.288s cat fb.hetBac1.chainHaeCon2Link.txt # 15974959 bases of 74374900 (21.479%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 haeCon2) > rbest.log 2>&1 & # real 0m45.750s # and for the swap: mkdir /hive/data/genomes/haeCon2/bed/blastz.hetBac1.swap cd /hive/data/genomes/haeCon2/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzHaeCon2.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m51.026s cat fb.haeCon2.chainHetBac1Link.txt # 23844390 bases of 346001353 (6.891%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` haeCon2 hetBac1) \ > rbest.log 2>&1 # real 1m49.908s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Loa loa/Eye worm - loaLoa1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzLoaLoa1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzLoaLoa1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs loaLoa1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Loa loa/Eye worm - loaLoa1 SEQ2_DIR=/hive/data/genomes/loaLoa1/loaLoa1.2bit SEQ2_LEN=/hive/data/genomes/loaLoa1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzLoaLoa1.2015-08-16 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 5m54.875s cat fb.hetBac1.chainLoaLoa1Link.txt # 6929677 bases of 74374900 (9.317%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 loaLoa1) > rbest.log 2>&1 & # real 0m29.961s # and for the swap: mkdir /hive/data/genomes/loaLoa1/bed/blastz.hetBac1.swap cd /hive/data/genomes/loaLoa1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzLoaLoa1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m59.405s cat fb.loaLoa1.chainHetBac1Link.txt # 6671489 bases of 87533141 (7.622%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` loaLoa1 hetBac1) \ > rbest.log 2>&1 # real 0m50.173s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Meloidogyne hapla/M. hapla - melHap1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzMelHap1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzMelHap1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs melHap1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Meloidogyne hapla/M. hapla - melHap1 SEQ2_DIR=/hive/data/genomes/melHap1/melHap1.2bit SEQ2_LEN=/hive/data/genomes/melHap1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzMelHap1.2015-08-16 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 3m51.586s cat fb.hetBac1.chainMelHap1Link.txt # 4212717 bases of 74374900 (5.664%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 melHap1) > rbest.log 2>&1 & # real 0m25.598s # and for the swap: mkdir /hive/data/genomes/melHap1/bed/blastz.hetBac1.swap cd /hive/data/genomes/melHap1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzMelHap1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m46.478s cat fb.melHap1.chainHetBac1Link.txt # 4084151 bases of 53017507 (7.703%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melHap1 hetBac1) \ > rbest.log 2>&1 # real 2m36.248s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Meloidogyne incognita/M. incognita - melInc2 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzMelInc2.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzMelInc2.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs melInc2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Meloidogyne incognita/M. incognita - melInc2 SEQ2_DIR=/hive/data/genomes/melInc2/melInc2.2bit SEQ2_LEN=/hive/data/genomes/melInc2/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzMelInc2.2015-08-16 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 5m0.415s cat fb.hetBac1.chainMelInc2Link.txt # 4109401 bases of 74374900 (5.525%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 melInc2) > rbest.log 2>&1 & # real 0m22.017s # and for the swap: mkdir /hive/data/genomes/melInc2/bed/blastz.hetBac1.swap cd /hive/data/genomes/melInc2/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzMelInc2.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m0.496s cat fb.melInc2.chainHetBac1Link.txt # 5212407 bases of 82114761 (6.348%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` melInc2 hetBac1) \ > rbest.log 2>&1 # real 5m13.010s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Necator americanus/N. americanus - necAme1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzNecAme1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzNecAme1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs necAme1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Necator americanus/N. americanus - necAme1 SEQ2_DIR=/hive/data/genomes/necAme1/necAme1.2bit SEQ2_LEN=/hive/data/genomes/necAme1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzNecAme1.2015-08-16 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 5m1.104s cat fb.hetBac1.chainNecAme1Link.txt # 16151454 bases of 74374900 (21.716%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 necAme1) > rbest.log 2>&1 & # real 0m45.472s # and for the swap: mkdir /hive/data/genomes/necAme1/bed/blastz.hetBac1.swap cd /hive/data/genomes/necAme1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzNecAme1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m53.584s cat fb.necAme1.chainHetBac1Link.txt # 17422961 bases of 208187215 (8.369%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` necAme1 hetBac1) \ > rbest.log 2>&1 # real 1m10.904s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Onchocerca volvulus/O. volvulus - oncVol1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzOncVol1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzOncVol1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs oncVol1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Onchocerca volvulus/O. volvulus - oncVol1 SEQ2_DIR=/hive/data/genomes/oncVol1/oncVol1.2bit SEQ2_LEN=/hive/data/genomes/oncVol1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzOncVol1.2015-08-16 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 5m11.638s cat fb.hetBac1.chainOncVol1Link.txt # 7115147 bases of 74374900 (9.567%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 oncVol1) > rbest.log 2>&1 & # real 0m45.665s # and for the swap: mkdir /hive/data/genomes/oncVol1/bed/blastz.hetBac1.swap cd /hive/data/genomes/oncVol1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzOncVol1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m9.060s cat fb.oncVol1.chainHetBac1Link.txt # 6991116 bases of 94327777 (7.412%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` oncVol1 hetBac1) \ > rbest.log 2>&1 # real 0m46.878s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Panagrellus redivivus/Microworm - panRed1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzPanRed1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzPanRed1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs panRed1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Panagrellus redivivus/Microworm - panRed1 SEQ2_DIR=/hive/data/genomes/panRed1/panRed1.2bit SEQ2_LEN=/hive/data/genomes/panRed1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzPanRed1.2015-08-16 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 5m0.022s cat fb.hetBac1.chainPanRed1Link.txt # 5112778 bases of 74374900 (6.874%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 panRed1) > rbest.log 2>&1 & # real 0m28.445s # and for the swap: mkdir /hive/data/genomes/panRed1/bed/blastz.hetBac1.swap cd /hive/data/genomes/panRed1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzPanRed1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 2m23.070s cat fb.panRed1.chainHetBac1Link.txt # 5028757 bases of 62228262 (8.081%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panRed1 hetBac1) \ > rbest.log 2>&1 # real 0m30.348s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Pristionchus exspectatus/P. exspectatus - priExs1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzPriExs1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzPriExs1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs priExs1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Pristionchus exspectatus/P. exspectatus - priExs1 SEQ2_DIR=/hive/data/genomes/priExs1/priExs1.2bit SEQ2_LEN=/hive/data/genomes/priExs1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzPriExs1.2015-08-16 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 2m58.560s cat fb.hetBac1.chainPriExs1Link.txt # 7322130 bases of 74374900 (9.845%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 priExs1) > rbest.log 2>&1 & # real 0m31.308s # and for the swap: mkdir /hive/data/genomes/priExs1/bed/blastz.hetBac1.swap cd /hive/data/genomes/priExs1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzPriExs1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 1m4.689s cat fb.priExs1.chainHetBac1Link.txt # 8542074 bases of 166917800 (5.118%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priExs1 hetBac1) \ > rbest.log 2>&1 # real 0m44.400s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Pristionchus pacificus/P. pacificus - priPac3 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzPriPac3.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzPriPac3.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs priPac3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Pristionchus pacificus/P. pacificus - priPac3 SEQ2_DIR=/hive/data/genomes/priPac3/priPac3.2bit SEQ2_LEN=/hive/data/genomes/priPac3/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzPriPac3.2015-08-16 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 7m39.614s cat fb.hetBac1.chainPriPac3Link.txt # 7339834 bases of 74374900 (9.869%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 priPac3) > rbest.log 2>&1 & # real 0m32.418s # and for the swap: mkdir /hive/data/genomes/priPac3/bed/blastz.hetBac1.swap cd /hive/data/genomes/priPac3/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzPriPac3.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m57.921s cat fb.priPac3.chainHetBac1Link.txt # 8129549 bases of 153238914 (5.305%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` priPac3 hetBac1) \ > rbest.log 2>&1 # real 4m47.411s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Strongyloides ratti/Threadworm - strRat2 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzStrRat2.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzStrRat2.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs strRat2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Strongyloides ratti/Threadworm - strRat2 SEQ2_DIR=/hive/data/genomes/strRat2/strRat2.2bit SEQ2_LEN=/hive/data/genomes/strRat2/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzStrRat2.2015-08-16 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 3m4.705s cat fb.hetBac1.chainStrRat2Link.txt # 4425357 bases of 74374900 (5.950%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 strRat2) > rbest.log 2>&1 & # real 0m27.645s # and for the swap: mkdir /hive/data/genomes/strRat2/bed/blastz.hetBac1.swap cd /hive/data/genomes/strRat2/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzStrRat2.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m43.843s cat fb.strRat2.chainHetBac1Link.txt # 4082188 bases of 43150242 (9.460%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` strRat2 hetBac1) \ > rbest.log 2>&1 # real 0m28.525s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Trichinella spiralis/Trichinella - triSpi1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzTriSpi1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzTriSpi1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs triSpi1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Trichinella spiralis/Trichinella - triSpi1 SEQ2_DIR=/hive/data/genomes/triSpi1/triSpi1.2bit SEQ2_LEN=/hive/data/genomes/triSpi1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzTriSpi1.2015-08-16 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 5m52.846s cat fb.hetBac1.chainTriSpi1Link.txt # 2805607 bases of 74374900 (3.772%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 triSpi1) > rbest.log 2>&1 & # real 0m26.112s # and for the swap: mkdir /hive/data/genomes/triSpi1/bed/blastz.hetBac1.swap cd /hive/data/genomes/triSpi1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzTriSpi1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 3m31.683s cat fb.triSpi1.chainHetBac1Link.txt # 2907272 bases of 58558192 (4.965%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSpi1 hetBac1) \ > rbest.log 2>&1 # real 0m57.143s ######################################################################## ######################################################################## # LASTZ Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 vs. # Trichuris suis/Whipworm - triSui1 # (DONE - 2015-08-16 - Hiram) mkdir /hive/data/genomes/hetBac1/bed/lastzTriSui1.2015-08-16 cd /hive/data/genomes/hetBac1/bed/lastzTriSui1.2015-08-16 cat << '_EOF_' > DEF # hetBac1 vs triSui1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_H=2000 BLASTZ_M=50 # TARGET:Heterorhabditis bacteriophora/H. bacteriophora/m31e - hetBac1 SEQ1_DIR=/hive/data/genomes/hetBac1/hetBac1.2bit SEQ1_LEN=/hive/data/genomes/hetBac1/chrom.sizes SEQ1_CHUNK=4000000 SEQ1_LAP=10000 SEQ1_LIMIT=100 # QUERY: Trichuris suis/Whipworm - triSui1 SEQ2_DIR=/hive/data/genomes/triSui1/triSui1.2bit SEQ2_LEN=/hive/data/genomes/triSui1/chrom.sizes SEQ2_CHUNK=4000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/hetBac1/bed/lastzTriSui1.2015-08-16 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 2m40.437s cat fb.hetBac1.chainTriSui1Link.txt # 2857377 bases of 74374900 (3.842%) in intersection time (doRecipBest.pl -buildDir=`pwd` hetBac1 triSui1) > rbest.log 2>&1 & # real 0m19.512s # and for the swap: mkdir /hive/data/genomes/triSui1/bed/blastz.hetBac1.swap cd /hive/data/genomes/triSui1/bed/blastz.hetBac1.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/hetBac1/bed/lastzTriSui1.2015-08-16/DEF \ -swap -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 0m44.817s cat fb.triSui1.chainHetBac1Link.txt # 2871809 bases of 71825323 (3.998%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` triSui1 hetBac1) \ > rbest.log 2>&1 # real 0m21.962s ########################################################################