6091558bab452de0ba020f3e08a9d20ef9aa3d81 hiram Wed Mar 18 19:09:58 2020 -0700 lastz runs for 12-way alignment on danRer10 per research request no redmine diff --git src/hg/makeDb/doc/galGal6/lastzRuns.txt src/hg/makeDb/doc/galGal6/lastzRuns.txt index f24c478..4badded 100644 --- src/hg/makeDb/doc/galGal6/lastzRuns.txt +++ src/hg/makeDb/doc/galGal6/lastzRuns.txt @@ -1,3974 +1,4047 @@ ############################################################################# # LASTZ chicken/galGal6 vs Rifleman/acaChl1 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16 printf "# chicken vs Rifleman # galGal6 vs acaChl1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: acaChl1 - Rifleman - Acanthisitta chloris SEQ2_DIR=/hive/data/genomes/acaChl1/acaChl1.2bit SEQ2_LEN=/hive/data/genomes/acaChl1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAcaChl1.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 641m40.810s cat fb.galGal6.chainAcaChl1Link.txt # 839072309 bases of 1055588482 (79.489%) in intersection cat fb.galGal6.chainSynAcaChl1Link.txt # 680540676 bases of 1055588482 (64.470%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AcaChl1) > rbest.log 2>&1 & # real 470m51.711s cat fb.galGal6.chainRBest.AcaChl1.txt # 740532507 bases of 1055588482 (70.154%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Japanese eel/angJap1 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16 printf "# chicken vs Japanese eel # galGal6 vs angJap1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: angJap1 - Japanese eel - Anguilla japonica SEQ2_DIR=/hive/data/genomes/angJap1/angJap1.2bit SEQ2_LEN=/hive/data/genomes/angJap1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAngJap1.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 157m11.534s cat fb.galGal6.chainAngJap1Link.txt # 57085539 bases of 1055588482 (5.408%) in intersection cat fb.galGal6.chainSynAngJap1Link.txt # 8699962 bases of 1055588482 (0.824%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AngJap1) > rbest.log 2>&1 & # real 85m42.406s cat fb.galGal6.chainRBest.AngJap1.txt # 43283102 bases of 1055588482 (4.100%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Stickleback/gasAcu1 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16 printf "# chicken vs Stickleback # galGal6 vs gasAcu1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: gasAcu1 - Stickleback - Gasterosteus aculeatus SEQ2_DIR=/hive/data/genomes/gasAcu1/gasAcu1.2bit SEQ2_LEN=/hive/data/genomes/gasAcu1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzGasAcu1.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 130m29.417s cat fb.galGal6.chainGasAcu1Link.txt # 48797842 bases of 1055588482 (4.623%) in intersection cat fb.galGal6.chainSynGasAcu1Link.txt # 13482396 bases of 1055588482 (1.277%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 GasAcu1) > rbest.log 2>&1 & # real 79m45.934s cat fb.galGal6.chainRBest.GasAcu1.txt # 38052220 bases of 1055588482 (3.605%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Turkey/melGal5 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16 printf "# chicken vs Turkey # galGal6 vs melGal5 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: melGal5 - Turkey - Meleagris gallopavo SEQ2_DIR=/hive/data/genomes/melGal5/melGal5.2bit SEQ2_LEN=/hive/data/genomes/melGal5/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzMelGal5.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 91m10.856s cat fb.galGal6.chainMelGal5Link.txt # 997476452 bases of 1055588482 (94.495%) in intersection cat fb.galGal6.chainSynMelGal5Link.txt # 715177000 bases of 1055588482 (67.751%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 MelGal5) > rbest.log 2>&1 & # real 251m2.883s cat fb.galGal6.chainRBest.MelGal5.txt # 909544688 bases of 1055588482 (86.165%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Lamprey/petMar3 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16 printf "# chicken vs Lamprey # galGal6 vs petMar3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: petMar3 - Lamprey - Petromyzon marinus SEQ2_DIR=/hive/data/genomes/petMar3/petMar3.2bit SEQ2_LEN=/hive/data/genomes/petMar3/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPetMar3.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 123m7.872s cat fb.galGal6.chainPetMar3Link.txt # 38618644 bases of 1055588482 (3.658%) in intersection cat fb.galGal6.chainSynPetMar3Link.txt # 1678799 bases of 1055588482 (0.159%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PetMar3) > rbest.log 2>&1 & # real 61m19.652s cat fb.galGal6.chainRBest.PetMar3.txt # 26040801 bases of 1055588482 (2.467%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs White-throated sparrow/zonAlb1 - (DONE - 2018-10-16 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16 cd /hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16 printf "# chicken vs White-throated sparrow # galGal6 vs zonAlb1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: zonAlb1 - White-throated sparrow - Zonotrichia albicollis SEQ2_DIR=/hive/data/genomes/zonAlb1/zonAlb1.2bit SEQ2_LEN=/hive/data/genomes/zonAlb1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzZonAlb1.2018-10-16 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 414m13.921s cat fb.galGal6.chainZonAlb1Link.txt # 830165711 bases of 1055588482 (78.645%) in intersection cat fb.galGal6.chainSynZonAlb1Link.txt # 694714801 bases of 1055588482 (65.813%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ZonAlb1) > rbest.log 2>&1 & # real 414m13.866s cat fb.galGal6.chainRBest.ZonAlb1.txt # 720721079 bases of 1055588482 (68.277%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs American alligator/allMis1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17 printf "# chicken vs American alligator # galGal6 vs allMis1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: allMis1 - American alligator - Alligator mississippiensis SEQ2_DIR=/hive/data/genomes/allMis1/allMis1.2bit SEQ2_LEN=/hive/data/genomes/allMis1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAllMis1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 368m30.696s cat fb.galGal6.chainAllMis1Link.txt # 472919428 bases of 1055588482 (44.801%) in intersection cat fb.galGal6.chainSynAllMis1Link.txt # 394401603 bases of 1055588482 (37.363%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AllMis1) > rbest.log 2>&1 & # real 231m5.251s cat fb.galGal6.chainRBest.AllMis1.txt # 432775108 bases of 1055588482 (40.998%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Chinese alligator/allSin1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17 printf "# chicken vs Chinese alligator # galGal6 vs allSin1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: allSin1 - Chinese alligator - Alligator sinensis SEQ2_DIR=/hive/data/genomes/allSin1/allSin1.2bit SEQ2_LEN=/hive/data/genomes/allSin1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAllSin1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 393m51.584s cat fb.galGal6.chainAllSin1Link.txt # 486162994 bases of 1055588482 (46.056%) in intersection cat fb.galGal6.chainSynAllSin1Link.txt # 406936492 bases of 1055588482 (38.551%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AllSin1) > rbest.log 2>&1 & # real 235m27.827s cat fb.galGal6.chainRBest.AllSin1.txt # 435270631 bases of 1055588482 (41.235%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Parrot/amaVit1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17 printf "# chicken vs Parrot # galGal6 vs amaVit1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: amaVit1 - Parrot - Amazona vittata SEQ2_DIR=/hive/data/genomes/amaVit1/amaVit1.2bit SEQ2_LEN=/hive/data/genomes/amaVit1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAmaVit1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 716m56.681s cat fb.galGal6.chainAmaVit1Link.txt # 850564670 bases of 1055588482 (80.577%) in intersection cat fb.galGal6.chainSynAmaVit1Link.txt # 570324827 bases of 1055588482 (54.029%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AmaVit1) > rbest.log 2>&1 & # real 514m10.579s cat fb.galGal6.chainRBest.AmaVit1.txt # 760058258 bases of 1055588482 (72.003%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Mallard duck/anaPla1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17 printf "# chicken vs Mallard duck # galGal6 vs anaPla1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: anaPla1 - Mallard duck - Anas platyrhynchos SEQ2_DIR=/hive/data/genomes/anaPla1/anaPla1.2bit SEQ2_LEN=/hive/data/genomes/anaPla1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAnaPla1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 624m1.292s cat fb.galGal6.chainAnaPla1Link.txt # 902625137 bases of 1055588482 (85.509%) in intersection cat fb.galGal6.chainSynAnaPla1Link.txt # 788255126 bases of 1055588482 (74.674%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AnaPla1) > rbest.log 2>&1 & # real 323m11.383s cat fb.galGal6.chainRBest.AnaPla1.txt # 811001997 bases of 1055588482 (76.829%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Lizard/anoCar2 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17 printf "# chicken vs Lizard # galGal6 vs anoCar2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: anoCar2 - Lizard - Anolis carolinensis SEQ2_DIR=/hive/data/genomes/anoCar2/anoCar2.2bit SEQ2_LEN=/hive/data/genomes/anoCar2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAnoCar2.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 499m17.964s cat fb.galGal6.chainAnoCar2Link.txt # 153349199 bases of 1055588482 (14.527%) in intersection cat fb.galGal6.chainSynAnoCar2Link.txt # 93909487 bases of 1055588482 (8.896%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AnoCar2) > rbest.log 2>&1 & # real 378m57.784s cat fb.galGal6.chainRBest.AnoCar2.txt # 121779211 bases of 1055588482 (11.537%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Spiny softshell turtle/apaSpi1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17 printf "# chicken vs Spiny softshell turtle # galGal6 vs apaSpi1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: apaSpi1 - Spiny softshell turtle - Apalone spinifera SEQ2_DIR=/hive/data/genomes/apaSpi1/apaSpi1.2bit SEQ2_LEN=/hive/data/genomes/apaSpi1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzApaSpi1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 848m10.616s cat fb.galGal6.chainApaSpi1Link.txt # 405079543 bases of 1055588482 (38.375%) in intersection cat fb.galGal6.chainSynApaSpi1Link.txt # 73623886 bases of 1055588482 (6.975%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ApaSpi1) > rbest.log 2>&1 & # real 635m31.914s cat fb.galGal6.chainRBest.ApaSpi1.txt # 345975149 bases of 1055588482 (32.776%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Bar tailed trogon/apaVit1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17 printf "# chicken vs Bar tailed trogon # galGal6 vs apaVit1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: apaVit1 - Bar tailed trogon - Apaloderma vittatum SEQ2_DIR=/hive/data/genomes/apaVit1/apaVit1.2bit SEQ2_LEN=/hive/data/genomes/apaVit1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzApaVit1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 666m21.837s cat fb.galGal6.chainApaVit1Link.txt # 855130988 bases of 1055588482 (81.010%) in intersection cat fb.galGal6.chainSynApaVit1Link.txt # 707907699 bases of 1055588482 (67.063%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ApaVit1) > rbest.log 2>&1 & # real 395m8.109s cat fb.galGal6.chainRBest.ApaVit1.txt # 768399443 bases of 1055588482 (72.793%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Emperor penguin/aptFor1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17 printf "# chicken vs Emperor penguin # galGal6 vs aptFor1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: aptFor1 - Emperor penguin - Aptenodytes forsteri SEQ2_DIR=/hive/data/genomes/aptFor1/aptFor1.2bit SEQ2_LEN=/hive/data/genomes/aptFor1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAptFor1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 482m48.347s cat fb.galGal6.chainAptFor1Link.txt # 916608502 bases of 1055588482 (86.834%) in intersection cat fb.galGal6.chainSynAptFor1Link.txt # 828156085 bases of 1055588482 (78.454%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AptFor1) > rbest.log 2>&1 & # real 222m3.219s cat fb.galGal6.chainRBest.AptFor1.txt # 840254605 bases of 1055588482 (79.601%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Golden eagle/aquChr2 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17 printf "# chicken vs Golden eagle # galGal6 vs aquChr2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: aquChr2 - Golden eagle - Aquila chrysaetos canadensis SEQ2_DIR=/hive/data/genomes/aquChr2/aquChr2.2bit SEQ2_LEN=/hive/data/genomes/aquChr2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAquChr2.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 446m55.621s cat fb.galGal6.chainAquChr2Link.txt # 925613456 bases of 1055588482 (87.687%) in intersection cat fb.galGal6.chainSynAquChr2Link.txt # 831330877 bases of 1055588482 (78.755%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AquChr2) > rbest.log 2>&1 & # real 232m0.358s cat fb.galGal6.chainRBest.AquChr2.txt # 848365224 bases of 1055588482 (80.369%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Scarlet macaw/araMac1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17 printf "# chicken vs Scarlet macaw # galGal6 vs araMac1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: araMac1 - Scarlet macaw - Ara macao SEQ2_DIR=/hive/data/genomes/araMac1/araMac1.2bit SEQ2_LEN=/hive/data/genomes/araMac1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzAraMac1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 890m2.745s cat fb.galGal6.chainAraMac1Link.txt # 804150969 bases of 1055588482 (76.180%) in intersection cat fb.galGal6.chainSynAraMac1Link.txt # 463740960 bases of 1055588482 (43.932%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 AraMac1) > rbest.log 2>&1 & # real 640m35.617s cat fb.galGal6.chainRBest.AraMac1.txt # 708288676 bases of 1055588482 (67.099%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Crowned crain/balPav1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17 printf "# chicken vs Crowned crain # galGal6 vs balPav1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: balPav1 - Crowned crain - Balearica pavonina gibbericeps SEQ2_DIR=/hive/data/genomes/balPav1/balPav1.2bit SEQ2_LEN=/hive/data/genomes/balPav1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzBalPav1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 520m25.509s cat fb.galGal6.chainBalPav1Link.txt # 893943891 bases of 1055588482 (84.687%) in intersection cat fb.galGal6.chainSynBalPav1Link.txt # 760199826 bases of 1055588482 (72.017%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 BalPav1) > rbest.log 2>&1 & # real 317m39.665s cat fb.galGal6.chainRBest.BalPav1.txt # 816345959 bases of 1055588482 (77.336%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Rhinoceros hornbill/bucRhi1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17 printf "# chicken vs Rhinoceros hornbill # galGal6 vs bucRhi1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: bucRhi1 - Rhinoceros hornbill - Buceros rhinoceros silvestris SEQ2_DIR=/hive/data/genomes/bucRhi1/bucRhi1.2bit SEQ2_LEN=/hive/data/genomes/bucRhi1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzBucRhi1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 621m43.314s cat fb.galGal6.chainBucRhi1Link.txt # 853039041 bases of 1055588482 (80.812%) in intersection cat fb.galGal6.chainSynBucRhi1Link.txt # 702565404 bases of 1055588482 (66.557%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 BucRhi1) > rbest.log 2>&1 & # real 409m2.624s cat fb.galGal6.chainRBest.BucRhi1.txt # 762575881 bases of 1055588482 (72.242%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Anna's hummingbird/calAnn1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17 printf "# chicken vs Anna's hummingbird # galGal6 vs calAnn1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: calAnn1 - Anna's hummingbird - Calypte anna SEQ2_DIR=/hive/data/genomes/calAnn1/calAnn1.2bit SEQ2_LEN=/hive/data/genomes/calAnn1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCalAnn1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 645m42.059s cat fb.galGal6.chainCalAnn1Link.txt # 841653301 bases of 1055588482 (79.733%) in intersection cat fb.galGal6.chainSynCalAnn1Link.txt # 708340584 bases of 1055588482 (67.104%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CalAnn1) > rbest.log 2>&1 & # real 402m36.129s cat fb.galGal6.chainRBest.CalAnn1.txt # 736578452 bases of 1055588482 (69.779%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Chuck-will's-widow/capCar1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17 printf "# chicken vs Chuck-will's-widow # galGal6 vs capCar1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: capCar1 - Chuck-will's-widow - Caprimulgus carolinensis SEQ2_DIR=/hive/data/genomes/capCar1/capCar1.2bit SEQ2_LEN=/hive/data/genomes/capCar1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCapCar1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 618m38.832s cat fb.galGal6.chainCapCar1Link.txt # 882181787 bases of 1055588482 (83.573%) in intersection cat fb.galGal6.chainSynCapCar1Link.txt # 724094046 bases of 1055588482 (68.596%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CapCar1) > rbest.log 2>&1 & # real 404m29.064s cat fb.galGal6.chainRBest.CapCar1.txt # 795678181 bases of 1055588482 (75.378%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Zebrafish/danRer11 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17 printf "# chicken vs Zebrafish # galGal6 vs danRer11 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: danRer11 - Zebrafish - Danio rerio SEQ2_DIR=/hive/data/genomes/danRer11/danRer11.2bit SEQ2_LEN=/hive/data/genomes/danRer11/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzDanRer11.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 288m51.949s cat fb.galGal6.chainDanRer11Link.txt # 67051784 bases of 1055588482 (6.352%) in intersection cat fb.galGal6.chainSynDanRer11Link.txt # 15220724 bases of 1055588482 (1.442%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 DanRer11) > rbest.log 2>&1 & # real 181m30.518s cat fb.galGal6.chainRBest.DanRer11.txt # 54875577 bases of 1055588482 (5.199%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Collared flycatcher/ficAlb2 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17 printf "# chicken vs Collared flycatcher # galGal6 vs ficAlb2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: ficAlb2 - Collared flycatcher - Ficedula albicollis SEQ2_DIR=/hive/data/genomes/ficAlb2/ficAlb2.2bit SEQ2_LEN=/hive/data/genomes/ficAlb2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzFicAlb2.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 916m56.403s cat fb.galGal6.chainFicAlb2Link.txt # 837654801 bases of 1055588482 (79.354%) in intersection cat fb.galGal6.chainSynFicAlb2Link.txt # 701981619 bases of 1055588482 (66.501%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 FicAlb2) > rbest.log 2>&1 & # real 687m21.884s cat fb.galGal6.chainRBest.FicAlb2.txt # 733810856 bases of 1055588482 (69.517%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Fugu/fr3 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17 printf "# chicken vs Fugu # galGal6 vs fr3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: fr3 - Fugu - Takifugu rubripes SEQ2_DIR=/hive/data/genomes/fr3/fr3.2bit SEQ2_LEN=/hive/data/genomes/fr3/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzFr3.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 89m47.854s cat fb.galGal6.chainFr3Link.txt # 42301582 bases of 1055588482 (4.007%) in intersection cat fb.galGal6.chainSynFr3Link.txt # 11843090 bases of 1055588482 (1.122%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 Fr3) > rbest.log 2>&1 & # real 56m3.102s cat fb.galGal6.chainRBest.Fr3.txt # 33236371 bases of 1055588482 (3.149%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Zebra finch/taeGut2 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17 printf "# chicken vs Zebra finch # galGal6 vs taeGut2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: taeGut2 - Zebra finch - Taeniopygia guttata SEQ2_DIR=/hive/data/genomes/taeGut2/taeGut2.2bit SEQ2_LEN=/hive/data/genomes/taeGut2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTaeGut2.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 483m53.121s cat fb.galGal6.chainTaeGut2Link.txt # 781017086 bases of 1055588482 (73.989%) in intersection cat fb.galGal6.chainSynTaeGut2Link.txt # 692861685 bases of 1055588482 (65.637%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TaeGut2) > rbest.log 2>&1 & # real 333m5.501s cat fb.galGal6.chainRBest.TaeGut2.txt # 718742085 bases of 1055588482 (68.089%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Tetraodon/tetNig1 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17 printf "# chicken vs Tetraodon # galGal6 vs tetNig1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tetNig1 - Tetraodon - Tetraodon nigroviridis SEQ2_DIR=/hive/data/genomes/tetNig1/tetNig1.2bit SEQ2_LEN=/hive/data/genomes/tetNig1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTetNig1.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 146m39.394s cat fb.galGal6.chainTetNig1Link.txt # 50235405 bases of 1055588482 (4.759%) in intersection cat fb.galGal6.chainSynTetNig1Link.txt # 11303688 bases of 1055588482 (1.071%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TetNig1) > rbest.log 2>&1 & # real 125m11.284s cat fb.galGal6.chainRBest.TetNig1.txt # 36506176 bases of 1055588482 (3.458%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs White throated tinamou/tinGut2 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17 printf "# chicken vs White throated tinamou # galGal6 vs tinGut2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tinGut2 - White throated tinamou - Tinamus guttatus SEQ2_DIR=/hive/data/genomes/tinGut2/tinGut2.2bit SEQ2_LEN=/hive/data/genomes/tinGut2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTinGut2.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 389m18.202s cat fb.galGal6.chainTinGut2Link.txt # 776674866 bases of 1055588482 (73.577%) in intersection cat fb.galGal6.chainSynTinGut2Link.txt # 660844755 bases of 1055588482 (62.604%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TinGut2) > rbest.log 2>&1 & # real 285m22.493s cat fb.galGal6.chainRBest.TinGut2.txt # 688296692 bases of 1055588482 (65.205%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs X. tropicalis/xenTro9 - (DONE - 2018-10-17 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17 cd /hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17 printf "# chicken vs X. tropicalis # galGal6 vs xenTro9 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: xenTro9 - X. tropicalis - Xenopus tropicalis SEQ2_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit SEQ2_LEN=/hive/data/genomes/xenTro9/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzXenTro9.2018-10-17 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 359m38.252s cat fb.galGal6.chainXenTro9Link.txt # 85528839 bases of 1055588482 (8.102%) in intersection cat fb.galGal6.chainSynXenTro9Link.txt # 41958665 bases of 1055588482 (3.975%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 XenTro9) > rbest.log 2>&1 & # real 250m49.764s cat fb.galGal6.chainRBest.XenTro9.txt # 66190094 bases of 1055588482 (6.270%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Red-legged seriema/carCri1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18 printf "# chicken vs Red-legged seriema # galGal6 vs carCri1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: carCri1 - Red-legged seriema - Cariama cristata SEQ2_DIR=/hive/data/genomes/carCri1/carCri1.2bit SEQ2_LEN=/hive/data/genomes/carCri1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCarCri1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 477m19.869s cat fb.galGal6.chainCarCri1Link.txt # 898243255 bases of 1055588482 (85.094%) in intersection cat fb.galGal6.chainSynCarCri1Link.txt # 766895002 bases of 1055588482 (72.651%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CarCri1) > rbest.log 2>&1 & # real 340m49.453s cat fb.galGal6.chainRBest.CarCri1.txt # 818808423 bases of 1055588482 (77.569%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Killdeer/chaVoc2 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18 printf "# chicken vs Killdeer # galGal6 vs chaVoc2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: chaVoc2 - Killdeer - Charadrius vociferus SEQ2_DIR=/hive/data/genomes/chaVoc2/chaVoc2.2bit SEQ2_LEN=/hive/data/genomes/chaVoc2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzChaVoc2.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 421m52.748s cat fb.galGal6.chainChaVoc2Link.txt # 910629364 bases of 1055588482 (86.267%) in intersection cat fb.galGal6.chainSynChaVoc2Link.txt # 813864162 bases of 1055588482 (77.101%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ChaVoc2) > rbest.log 2>&1 & # real 242m34.087s cat fb.galGal6.chainRBest.ChaVoc2.txt # 833063294 bases of 1055588482 (78.919%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Green seaturtle/cheMyd1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18 printf "# chicken vs Green seaturtle # galGal6 vs cheMyd1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: cheMyd1 - Green seaturtle - Chelonia mydas SEQ2_DIR=/hive/data/genomes/cheMyd1/cheMyd1.2bit SEQ2_LEN=/hive/data/genomes/cheMyd1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCheMyd1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 488m23.776s cat fb.galGal6.chainCheMyd1Link.txt # 538550235 bases of 1055588482 (51.019%) in intersection cat fb.galGal6.chainSynCheMyd1Link.txt # 439571636 bases of 1055588482 (41.642%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CheMyd1) > rbest.log 2>&1 & # real 356m1.191s cat fb.galGal6.chainRBest.CheMyd1.txt # 484498431 bases of 1055588482 (45.898%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Houbara bustard/chlUnd1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18 printf "# chicken vs Houbara bustard # galGal6 vs chlUnd1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: chlUnd1 - Houbara bustard - Chlamydotis undulata macqueenii SEQ2_DIR=/hive/data/genomes/chlUnd1/chlUnd1.2bit SEQ2_LEN=/hive/data/genomes/chlUnd1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzChlUnd1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 444m5.490s cat fb.galGal6.chainChlUnd1Link.txt # 876572094 bases of 1055588482 (83.041%) in intersection cat fb.galGal6.chainSynChlUnd1Link.txt # 728906002 bases of 1055588482 (69.052%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ChlUnd1) > rbest.log 2>&1 & # real 315m54.274s cat fb.galGal6.chainRBest.ChlUnd1.txt # 792837683 bases of 1055588482 (75.109%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Painted turtle/chrPic2 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18 printf "# chicken vs Painted turtle # galGal6 vs chrPic2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: chrPic2 - Painted turtle - Chrysemys picta bellii SEQ2_DIR=/hive/data/genomes/chrPic2/chrPic2.2bit SEQ2_LEN=/hive/data/genomes/chrPic2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzChrPic2.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 499m8.294s cat fb.galGal6.chainChrPic2Link.txt # 545995699 bases of 1055588482 (51.724%) in intersection cat fb.galGal6.chainSynChrPic2Link.txt # 441949079 bases of 1055588482 (41.868%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ChrPic2) > rbest.log 2>&1 & # real 392m57.089s cat fb.galGal6.chainRBest.ChrPic2.txt # 489464915 bases of 1055588482 (46.369%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Rock pigeon/colLiv1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18 printf "# chicken vs Rock pigeon # galGal6 vs colLiv1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: colLiv1 - Rock pigeon - Columba livia SEQ2_DIR=/hive/data/genomes/colLiv1/colLiv1.2bit SEQ2_LEN=/hive/data/genomes/colLiv1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzColLiv1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 477m10.507s cat fb.galGal6.chainColLiv1Link.txt # 876908494 bases of 1055588482 (83.073%) in intersection cat fb.galGal6.chainSynColLiv1Link.txt # 766031947 bases of 1055588482 (72.569%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ColLiv1) > rbest.log 2>&1 & # real 314m13.764s cat fb.galGal6.chainRBest.ColLiv1.txt # 785036429 bases of 1055588482 (74.370%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Speckled mousebird/colStr1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18 printf "# chicken vs Speckled mousebird # galGal6 vs colStr1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: colStr1 - Speckled mousebird - Colius striatus SEQ2_DIR=/hive/data/genomes/colStr1/colStr1.2bit SEQ2_LEN=/hive/data/genomes/colStr1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzColStr1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 587m56.997s cat fb.galGal6.chainColStr1Link.txt # 854884790 bases of 1055588482 (80.987%) in intersection cat fb.galGal6.chainSynColStr1Link.txt # 678861985 bases of 1055588482 (64.311%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ColStr1) > rbest.log 2>&1 & # real 441m29.228s cat fb.galGal6.chainRBest.ColStr1.txt # 760238251 bases of 1055588482 (72.020%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs American crow/corBra1 - (DONE - 2018-10-18 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18 cd /hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18 printf "# chicken vs American crow # galGal6 vs corBra1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: corBra1 - American crow - Corvus brachyrhynchos SEQ2_DIR=/hive/data/genomes/corBra1/corBra1.2bit SEQ2_LEN=/hive/data/genomes/corBra1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCorBra1.2018-10-18 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 565m41.665s cat fb.galGal6.chainCorBra1Link.txt # 854798756 bases of 1055588482 (80.978%) in intersection cat fb.galGal6.chainSynCorBra1Link.txt # 732338012 bases of 1055588482 (69.377%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CorBra1) > rbest.log 2>&1 & # real 392m5.064s cat fb.galGal6.chainRBest.CorBra1.txt # 754104139 bases of 1055588482 (71.439%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Hooded crow/corCor1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19 printf "# chicken vs Hooded crow # galGal6 vs corCor1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: corCor1 - Hooded crow - Corvus cornix cornix SEQ2_DIR=/hive/data/genomes/corCor1/corCor1.2bit SEQ2_LEN=/hive/data/genomes/corCor1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCorCor1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 591m45.748s cat fb.galGal6.chainCorCor1Link.txt # 850530295 bases of 1055588482 (80.574%) in intersection cat fb.galGal6.chainSynCorCor1Link.txt # 718475664 bases of 1055588482 (68.064%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CorCor1) > rbest.log 2>&1 & # real 425m28.944s cat fb.galGal6.chainRBest.CorCor1.txt # 750021584 bases of 1055588482 (71.052%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Japanese quail/cotJap1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19 printf "# chicken vs Japanese quail # galGal6 vs cotJap1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: cotJap1 - Japanese quail - Coturnix japonica SEQ2_DIR=/hive/data/genomes/cotJap1/cotJap1.2bit SEQ2_LEN=/hive/data/genomes/cotJap1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCotJap1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 402m14.191s cat fb.galGal6.chainCotJap1Link.txt # 592408208 bases of 1055588482 (56.121%) in intersection cat fb.galGal6.chainSynCotJap1Link.txt # 428571708 bases of 1055588482 (40.600%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CotJap1) > rbest.log 2>&1 & # real 331m41.351s cat fb.galGal6.chainRBest.CotJap1.txt # 431816963 bases of 1055588482 (40.908%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Common cuckoo/cucCan1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19 printf "# chicken vs Common cuckoo # galGal6 vs cucCan1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: cucCan1 - Common cuckoo - Cuculus canorus SEQ2_DIR=/hive/data/genomes/cucCan1/cucCan1.2bit SEQ2_LEN=/hive/data/genomes/cucCan1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCucCan1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 495m53.604s cat fb.galGal6.chainCucCan1Link.txt # 877724050 bases of 1055588482 (83.150%) in intersection cat fb.galGal6.chainSynCucCan1Link.txt # 761013196 bases of 1055588482 (72.094%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CucCan1) > rbest.log 2>&1 & # real 330m35.696s cat fb.galGal6.chainRBest.CucCan1.txt # 784860736 bases of 1055588482 (74.353%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Little egret/egrGar1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19 printf "# chicken vs Little egret # galGal6 vs egrGar1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: egrGar1 - Little egret - Egretta garzetta SEQ2_DIR=/hive/data/genomes/egrGar1/egrGar1.2bit SEQ2_LEN=/hive/data/genomes/egrGar1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzEgrGar1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 380m24.844s cat fb.galGal6.chainEgrGar1Link.txt # 903470826 bases of 1055588482 (85.589%) in intersection cat fb.galGal6.chainSynEgrGar1Link.txt # 807513965 bases of 1055588482 (76.499%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 EgrGar1) > rbest.log 2>&1 & # real 242m14.176s cat fb.galGal6.chainRBest.EgrGar1.txt # 823806797 bases of 1055588482 (78.042%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Sunbittern/eurHel1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19 printf "# chicken vs Sunbittern # galGal6 vs eurHel1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: eurHel1 - Sunbittern - Eurypyga helias SEQ2_DIR=/hive/data/genomes/eurHel1/eurHel1.2bit SEQ2_LEN=/hive/data/genomes/eurHel1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzEurHel1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 691m55.179s cat fb.galGal6.chainEurHel1Link.txt # 870082807 bases of 1055588482 (82.426%) in intersection cat fb.galGal6.chainSynEurHel1Link.txt # 714159632 bases of 1055588482 (67.655%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 EurHel1) > rbest.log 2>&1 & # real 387m45.136s cat fb.galGal6.chainRBest.EurHel1.txt # 783796534 bases of 1055588482 (74.252%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Saker falcon/falChe1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19 printf "# chicken vs Saker falcon # galGal6 vs falChe1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: falChe1 - Saker falcon - Falco cherrug SEQ2_DIR=/hive/data/genomes/falChe1/falChe1.2bit SEQ2_LEN=/hive/data/genomes/falChe1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzFalChe1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 624m12.224s cat fb.galGal6.chainFalChe1Link.txt # 911415065 bases of 1055588482 (86.342%) in intersection cat fb.galGal6.chainSynFalChe1Link.txt # 807507886 bases of 1055588482 (76.498%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 FalChe1) > rbest.log 2>&1 & # real 273m9.858s cat fb.galGal6.chainRBest.FalChe1.txt # 828810487 bases of 1055588482 (78.516%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Peregrine falcon/falPer1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19 printf "# chicken vs Peregrine falcon # galGal6 vs falPer1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: falPer1 - Peregrine falcon - Falco peregrinus SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzFalPer1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 625m24.573s cat fb.galGal6.chainFalPer1Link.txt # 913080823 bases of 1055588482 (86.500%) in intersection cat fb.galGal6.chainSynFalPer1Link.txt # 812447015 bases of 1055588482 (76.966%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 FalPer1) > rbest.log 2>&1 & # real 274m12.882s cat fb.galGal6.chainRBest.FalPer1.txt # 830510373 bases of 1055588482 (78.677%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Northern fulmar/fulGla1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19 printf "# chicken vs Northern fulmar # galGal6 vs fulGla1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: fulGla1 - Northern fulmar - Fulmarus glacialis SEQ2_DIR=/hive/data/genomes/fulGla1/fulGla1.2bit SEQ2_LEN=/hive/data/genomes/fulGla1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzFulGla1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 599m13.056s cat fb.galGal6.chainFulGla1Link.txt # 900756652 bases of 1055588482 (85.332%) in intersection cat fb.galGal6.chainSynFulGla1Link.txt # 771539763 bases of 1055588482 (73.091%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 FulGla1) > rbest.log 2>&1 & # real 300m46.949s cat fb.galGal6.chainRBest.FulGla1.txt # 824502605 bases of 1055588482 (78.108%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Red-throated loon/gavSte1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19 printf "# chicken vs Red-throated loon # galGal6 vs gavSte1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: gavSte1 - Red-throated loon - Gavia stellata SEQ2_DIR=/hive/data/genomes/gavSte1/gavSte1.2bit SEQ2_LEN=/hive/data/genomes/gavSte1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzGavSte1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 612m10.148s cat fb.galGal6.chainGavSte1Link.txt # 894263882 bases of 1055588482 (84.717%) in intersection cat fb.galGal6.chainSynGavSte1Link.txt # 761960610 bases of 1055588482 (72.183%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 GavSte1) > rbest.log 2>&1 & # real 314m22.814s cat fb.galGal6.chainRBest.GavSte1.txt # 818435214 bases of 1055588482 (77.534%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Medium ground finch/geoFor1 - (DONE - 2018-10-19 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19 cd /hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19 printf "# chicken vs Medium ground finch # galGal6 vs geoFor1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: geoFor1 - Medium ground finch - Geospiza fortis SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzGeoFor1.2018-10-19 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 765m20.987s cat fb.galGal6.chainGeoFor1Link.txt # 837073388 bases of 1055588482 (79.299%) in intersection cat fb.galGal6.chainSynGeoFor1Link.txt # 706945549 bases of 1055588482 (66.972%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 GeoFor1) > rbest.log 2>&1 & # real 423m23.442s cat fb.galGal6.chainRBest.GeoFor1.txt # 731219352 bases of 1055588482 (69.271%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs White-tailed eagle/halAlb1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20 printf "# chicken vs White-tailed eagle # galGal6 vs halAlb1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: halAlb1 - White-tailed eagle - Haliaeetus albicilla SEQ2_DIR=/hive/data/genomes/halAlb1/halAlb1.2bit SEQ2_LEN=/hive/data/genomes/halAlb1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzHalAlb1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 425m10.485s cat fb.galGal6.chainHalAlb1Link.txt # 897213301 bases of 1055588482 (84.997%) in intersection cat fb.galGal6.chainSynHalAlb1Link.txt # 772402407 bases of 1055588482 (73.173%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 HalAlb1) > rbest.log 2>&1 & # real 299m24.177s cat fb.galGal6.chainRBest.HalAlb1.txt # 819350653 bases of 1055588482 (77.620%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Bald eagle/halLeu1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20 printf "# chicken vs Bald eagle # galGal6 vs halLeu1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: halLeu1 - Bald eagle - Haliaeetus leucocephalus SEQ2_DIR=/hive/data/genomes/halLeu1/halLeu1.2bit SEQ2_LEN=/hive/data/genomes/halLeu1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzHalLeu1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 384m24.469s cat fb.galGal6.chainHalLeu1Link.txt # 917551459 bases of 1055588482 (86.923%) in intersection cat fb.galGal6.chainSynHalLeu1Link.txt # 820998974 bases of 1055588482 (77.776%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 HalLeu1) > rbest.log 2>&1 & # real 247m10.238s cat fb.galGal6.chainRBest.HalLeu1.txt # 838255932 bases of 1055588482 (79.411%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Cuckoo roller/lepDis1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20 printf "# chicken vs Cuckoo roller # galGal6 vs lepDis1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: lepDis1 - Cuckoo roller - Leptosomus discolor SEQ2_DIR=/hive/data/genomes/lepDis1/lepDis1.2bit SEQ2_LEN=/hive/data/genomes/lepDis1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzLepDis1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 483m47.811s cat fb.galGal6.chainLepDis1Link.txt # 897470746 bases of 1055588482 (85.021%) in intersection cat fb.galGal6.chainSynLepDis1Link.txt # 763954799 bases of 1055588482 (72.372%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 LepDis1) > rbest.log 2>&1 & # real 346m34.314s cat fb.galGal6.chainRBest.LepDis1.txt # 818033338 bases of 1055588482 (77.495%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Arctic lamprey/letCam1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20 printf "# chicken vs Arctic lamprey # galGal6 vs letCam1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: letCam1 - Arctic lamprey - Lethenteron camtschaticum SEQ2_DIR=/hive/data/genomes/letCam1/letCam1.2bit SEQ2_LEN=/hive/data/genomes/letCam1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzLetCam1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 87m59.672s cat fb.galGal6.chainLetCam1Link.txt # 35206160 bases of 1055588482 (3.335%) in intersection cat fb.galGal6.chainSynLetCam1Link.txt # 1547533 bases of 1055588482 (0.147%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 LetCam1) > rbest.log 2>&1 & # real 57m29.804s cat fb.galGal6.chainRBest.LetCam1.txt # 23080040 bases of 1055588482 (2.186%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Zebra mbuna/mayZeb1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20 printf "# chicken vs Zebra mbuna # galGal6 vs mayZeb1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: mayZeb1 - Zebra mbuna - Maylandia zebra SEQ2_DIR=/hive/data/genomes/mayZeb1/mayZeb1.2bit SEQ2_LEN=/hive/data/genomes/mayZeb1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzMayZeb1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 95m40.688s cat fb.galGal6.chainMayZeb1Link.txt # 47913341 bases of 1055588482 (4.539%) in intersection cat fb.galGal6.chainSynMayZeb1Link.txt # 14297083 bases of 1055588482 (1.354%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 MayZeb1) > rbest.log 2>&1 & # real 67m51.802s cat fb.galGal6.chainRBest.MayZeb1.txt # 39264653 bases of 1055588482 (3.720%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Budgerigar/melUnd1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20 printf "# chicken vs Budgerigar # galGal6 vs melUnd1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: melUnd1 - Budgerigar - Melopsittacus undulatus SEQ2_DIR=/hive/data/genomes/melUnd1/melUnd1.2bit SEQ2_LEN=/hive/data/genomes/melUnd1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzMelUnd1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 578m59.698s cat fb.galGal6.chainMelUnd1Link.txt # 862351682 bases of 1055588482 (81.694%) in intersection cat fb.galGal6.chainSynMelUnd1Link.txt # 737018487 bases of 1055588482 (69.821%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 MelUnd1) > rbest.log 2>&1 & # real 424m30.658s cat fb.galGal6.chainRBest.MelUnd1.txt # 765760426 bases of 1055588482 (72.543%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Northern carmine bee-eater/merNub1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20 printf "# chicken vs Northern carmine bee-eater # galGal6 vs merNub1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: merNub1 - Northern carmine bee-eater - Merops nubicus SEQ2_DIR=/hive/data/genomes/merNub1/merNub1.2bit SEQ2_LEN=/hive/data/genomes/merNub1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzMerNub1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 609m53.704s cat fb.galGal6.chainMerNub1Link.txt # 855219539 bases of 1055588482 (81.018%) in intersection cat fb.galGal6.chainSynMerNub1Link.txt # 689682468 bases of 1055588482 (65.336%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 MerNub1) > rbest.log 2>&1 & # real 461m12.202s cat fb.galGal6.chainRBest.MerNub1.txt # 762543217 bases of 1055588482 (72.239%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Brown roatelo/mesUni1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20 printf "# chicken vs Brown roatelo # galGal6 vs mesUni1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: mesUni1 - Brown roatelo - Mesitornis unicolor SEQ2_DIR=/hive/data/genomes/mesUni1/mesUni1.2bit SEQ2_LEN=/hive/data/genomes/mesUni1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzMesUni1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 515m50.332s cat fb.galGal6.chainMesUni1Link.txt # 872437783 bases of 1055588482 (82.649%) in intersection cat fb.galGal6.chainSynMesUni1Link.txt # 712722916 bases of 1055588482 (67.519%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 MesUni1) > rbest.log 2>&1 & # real 382m17.567s cat fb.galGal6.chainRBest.MesUni1.txt # 780887325 bases of 1055588482 (73.976%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Tibetan frog/nanPar1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20 printf "# chicken vs Tibetan frog # galGal6 vs nanPar1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: nanPar1 - Tibetan frog - Nanorana parkeri SEQ2_DIR=/hive/data/genomes/nanPar1/nanPar1.2bit SEQ2_LEN=/hive/data/genomes/nanPar1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzNanPar1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 246m50.610s cat fb.galGal6.chainNanPar1Link.txt # 79844603 bases of 1055588482 (7.564%) in intersection cat fb.galGal6.chainSynNanPar1Link.txt # 32681061 bases of 1055588482 (3.096%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 NanPar1) > rbest.log 2>&1 & # real 114m3.839s cat fb.galGal6.chainRBest.NanPar1.txt # 60765484 bases of 1055588482 (5.757%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Crested ibis/nipNip1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20 printf "# chicken vs Crested ibis # galGal6 vs nipNip1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: nipNip1 - Crested ibis - Nipponia nippon SEQ2_DIR=/hive/data/genomes/nipNip1/nipNip1.2bit SEQ2_LEN=/hive/data/genomes/nipNip1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzNipNip1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 468m6.512s cat fb.galGal6.chainNipNip1Link.txt # 917340936 bases of 1055588482 (86.903%) in intersection cat fb.galGal6.chainSynNipNip1Link.txt # 816164720 bases of 1055588482 (77.318%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 NipNip1) > rbest.log 2>&1 & # real 258m34.526s cat fb.galGal6.chainRBest.NipNip1.txt # 839113287 bases of 1055588482 (79.492%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Hoatzin/opiHoa1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20 printf "# chicken vs Hoatzin # galGal6 vs opiHoa1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: opiHoa1 - Hoatzin - Opisthocomus hoazin SEQ2_DIR=/hive/data/genomes/opiHoa1/opiHoa1.2bit SEQ2_LEN=/hive/data/genomes/opiHoa1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzOpiHoa1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 489m5.171s cat fb.galGal6.chainOpiHoa1Link.txt # 892802003 bases of 1055588482 (84.579%) in intersection cat fb.galGal6.chainSynOpiHoa1Link.txt # 789312550 bases of 1055588482 (74.775%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 OpiHoa1) > rbest.log 2>&1 & # real 283m23.426s cat fb.galGal6.chainRBest.OpiHoa1.txt # 810599536 bases of 1055588482 (76.791%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Nile tilapia/oreNil3 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20 printf "# chicken vs Nile tilapia # galGal6 vs oreNil3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: oreNil3 - Nile tilapia - Oreochromis niloticus SEQ2_DIR=/hive/data/genomes/oreNil3/oreNil3.2bit SEQ2_LEN=/hive/data/genomes/oreNil3/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzOreNil3.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 145m20.448s cat fb.galGal6.chainOreNil3Link.txt # 51982658 bases of 1055588482 (4.925%) in intersection cat fb.galGal6.chainSynOreNil3Link.txt # 15123869 bases of 1055588482 (1.433%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 OreNil3) > rbest.log 2>&1 & # real 109m35.337s cat fb.galGal6.chainRBest.OreNil3.txt # 42938334 bases of 1055588482 (4.068%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Medaka/oryLat2 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20 printf "# chicken vs Medaka # galGal6 vs oryLat2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: oryLat2 - Medaka - Oryzias latipes SEQ2_DIR=/hive/data/genomes/oryLat2/oryLat2.2bit SEQ2_LEN=/hive/data/genomes/oryLat2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzOryLat2.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 115m40.641s cat fb.galGal6.chainOryLat2Link.txt # 48185568 bases of 1055588482 (4.565%) in intersection cat fb.galGal6.chainSynOryLat2Link.txt # 12103669 bases of 1055588482 (1.147%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 OryLat2) > rbest.log 2>&1 & # real 86m59.599s cat fb.galGal6.chainRBest.OryLat2.txt # 37955179 bases of 1055588482 (3.596%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Dalmatian pelican/pelCri1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20 printf "# chicken vs Dalmatian pelican # galGal6 vs pelCri1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pelCri1 - Dalmatian pelican - Pelecanus crispus SEQ2_DIR=/hive/data/genomes/pelCri1/pelCri1.2bit SEQ2_LEN=/hive/data/genomes/pelCri1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPelCri1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 448m45.276s cat fb.galGal6.chainPelCri1Link.txt # 900882646 bases of 1055588482 (85.344%) in intersection cat fb.galGal6.chainSynPelCri1Link.txt # 761992182 bases of 1055588482 (72.186%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PelCri1) > rbest.log 2>&1 & # real 321m51.723s cat fb.galGal6.chainRBest.PelCri1.txt # 825489194 bases of 1055588482 (78.202%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Chinese softshell turtle/pelSin1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20 printf "# chicken vs Chinese softshell turtle # galGal6 vs pelSin1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pelSin1 - Chinese softshell turtle - Pelodiscus sinensis SEQ2_DIR=/hive/data/genomes/pelSin1/pelSin1.2bit SEQ2_LEN=/hive/data/genomes/pelSin1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPelSin1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 606m19.155s cat fb.galGal6.chainPelSin1Link.txt # 443193142 bases of 1055588482 (41.985%) in intersection cat fb.galGal6.chainSynPelSin1Link.txt # 328819719 bases of 1055588482 (31.150%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PelSin1) > rbest.log 2>&1 & # real 462m36.209s cat fb.galGal6.chainRBest.PelSin1.txt # 379282279 bases of 1055588482 (35.931%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Great cormorant/phaCar1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20 printf "# chicken vs Great cormorant # galGal6 vs phaCar1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: phaCar1 - Great cormorant - Phalacrocorax carbo SEQ2_DIR=/hive/data/genomes/phaCar1/phaCar1.2bit SEQ2_LEN=/hive/data/genomes/phaCar1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPhaCar1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 521m40.317s cat fb.galGal6.chainPhaCar1Link.txt # 888618683 bases of 1055588482 (84.182%) in intersection cat fb.galGal6.chainSynPhaCar1Link.txt # 748304742 bases of 1055588482 (70.890%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PhaCar1) > rbest.log 2>&1 & # real 336m56.098s cat fb.galGal6.chainRBest.PhaCar1.txt # 812143245 bases of 1055588482 (76.937%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs White-tailed tropicbird/phaLep1 - (DONE - 2018-10-20 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20 cd /hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20 printf "# chicken vs White-tailed tropicbird # galGal6 vs phaLep1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: phaLep1 - White-tailed tropicbird - Phaethon lepturus SEQ2_DIR=/hive/data/genomes/phaLep1/phaLep1.2bit SEQ2_LEN=/hive/data/genomes/phaLep1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPhaLep1.2018-10-20 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 522m18.477s cat fb.galGal6.chainPhaLep1Link.txt # 892174920 bases of 1055588482 (84.519%) in intersection cat fb.galGal6.chainSynPhaLep1Link.txt # 748102047 bases of 1055588482 (70.871%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PhaLep1) > rbest.log 2>&1 & # real 348m19.903s cat fb.galGal6.chainRBest.PhaLep1.txt # 815574374 bases of 1055588482 (77.263%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs American flamingo/phoRub1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21 printf "# chicken vs American flamingo # galGal6 vs phoRub1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: phoRub1 - American flamingo - Phoenicopterus ruber ruber SEQ2_DIR=/hive/data/genomes/phoRub1/phoRub1.2bit SEQ2_LEN=/hive/data/genomes/phoRub1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPhoRub1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 453m3.724s cat fb.galGal6.chainPhoRub1Link.txt # 895062456 bases of 1055588482 (84.793%) in intersection cat fb.galGal6.chainSynPhoRub1Link.txt # 747746047 bases of 1055588482 (70.837%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PhoRub1) > rbest.log 2>&1 & # real 320m1.593s cat fb.galGal6.chainRBest.PhoRub1.txt # 820973879 bases of 1055588482 (77.774%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Downy woodpecker/picPub1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21 printf "# chicken vs Downy woodpecker # galGal6 vs picPub1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: picPub1 - Downy woodpecker - Picoides pubescens SEQ2_DIR=/hive/data/genomes/picPub1/picPub1.2bit SEQ2_LEN=/hive/data/genomes/picPub1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPicPub1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 707m2.631s cat fb.galGal6.chainPicPub1Link.txt # 783855965 bases of 1055588482 (74.258%) in intersection cat fb.galGal6.chainSynPicPub1Link.txt # 638057644 bases of 1055588482 (60.446%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PicPub1) > rbest.log 2>&1 & # real 557m15.590s cat fb.galGal6.chainRBest.PicPub1.txt # 673786174 bases of 1055588482 (63.830%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Tibetan ground jay/pseHum1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21 printf "# chicken vs Tibetan ground jay # galGal6 vs pseHum1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pseHum1 - Tibetan ground jay - Pseudopodoces humilis SEQ2_DIR=/hive/data/genomes/pseHum1/pseHum1.2bit SEQ2_LEN=/hive/data/genomes/pseHum1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPseHum1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 657m45.610s cat fb.galGal6.chainPseHum1Link.txt # 851036997 bases of 1055588482 (80.622%) in intersection cat fb.galGal6.chainSynPseHum1Link.txt # 717648839 bases of 1055588482 (67.986%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PseHum1) > rbest.log 2>&1 & # real 478m33.407s cat fb.galGal6.chainRBest.PseHum1.txt # 747040317 bases of 1055588482 (70.770%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Yellow-throated sandgrouse/pteGut1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21 printf "# chicken vs Yellow-throated sandgrouse # galGal6 vs pteGut1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pteGut1 - Yellow-throated sandgrouse - Pterocles gutturalis SEQ2_DIR=/hive/data/genomes/pteGut1/pteGut1.2bit SEQ2_LEN=/hive/data/genomes/pteGut1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPteGut1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 484m8.206s cat fb.galGal6.chainPteGut1Link.txt # 871105195 bases of 1055588482 (82.523%) in intersection cat fb.galGal6.chainSynPteGut1Link.txt # 727109988 bases of 1055588482 (68.882%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PteGut1) > rbest.log 2>&1 & # real 344m37.225s cat fb.galGal6.chainRBest.PteGut1.txt # 784577743 bases of 1055588482 (74.326%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Adelie penguin/pygAde1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21 printf "# chicken vs Adelie penguin # galGal6 vs pygAde1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pygAde1 - Adelie penguin - Pygoscelis adeliae SEQ2_DIR=/hive/data/genomes/pygAde1/pygAde1.2bit SEQ2_LEN=/hive/data/genomes/pygAde1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPygAde1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 375m37.220s cat fb.galGal6.chainPygAde1Link.txt # 906663676 bases of 1055588482 (85.892%) in intersection cat fb.galGal6.chainSynPygAde1Link.txt # 820549396 bases of 1055588482 (77.734%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PygAde1) > rbest.log 2>&1 & # real 225m31.093s cat fb.galGal6.chainRBest.PygAde1.txt # 832234764 bases of 1055588482 (78.841%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Burmese python/pytBiv1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21 printf "# chicken vs Burmese python # galGal6 vs pytBiv1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: pytBiv1 - Burmese python - Python bivittatus SEQ2_DIR=/hive/data/genomes/pytBiv1/pytBiv1.2bit SEQ2_LEN=/hive/data/genomes/pytBiv1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzPytBiv1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 324m31.677s cat fb.galGal6.chainPytBiv1Link.txt # 166849799 bases of 1055588482 (15.806%) in intersection cat fb.galGal6.chainSynPytBiv1Link.txt # 71801031 bases of 1055588482 (6.802%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 PytBiv1) > rbest.log 2>&1 & # real 268m26.640s cat fb.galGal6.chainRBest.PytBiv1.txt # 125015534 bases of 1055588482 (11.843%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Canary/serCan1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21 printf "# chicken vs Canary # galGal6 vs serCan1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: serCan1 - Canary - Serinus canaria SEQ2_DIR=/hive/data/genomes/serCan1/serCan1.2bit SEQ2_LEN=/hive/data/genomes/serCan1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzSerCan1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 717m30.966s cat fb.galGal6.chainSerCan1Link.txt # 843441693 bases of 1055588482 (79.903%) in intersection cat fb.galGal6.chainSynSerCan1Link.txt # 699854918 bases of 1055588482 (66.300%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 SerCan1) > rbest.log 2>&1 & # real 522m59.796s cat fb.galGal6.chainRBest.SerCan1.txt # 733176559 bases of 1055588482 (69.457%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Ostrich/strCam1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21 printf "# chicken vs Ostrich # galGal6 vs strCam1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: strCam1 - Ostrich - Struthio camelus australis SEQ2_DIR=/hive/data/genomes/strCam1/strCam1.2bit SEQ2_LEN=/hive/data/genomes/strCam1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzStrCam1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 363m35.472s cat fb.galGal6.chainStrCam1Link.txt # 869691537 bases of 1055588482 (82.389%) in intersection cat fb.galGal6.chainSynStrCam1Link.txt # 787385857 bases of 1055588482 (74.592%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 StrCam1) > rbest.log 2>&1 & # real 205m25.277s cat fb.galGal6.chainRBest.StrCam1.txt # 800156430 bases of 1055588482 (75.802%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Red crested turaco/tauEry1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21 printf "# chicken vs Red crested turaco # galGal6 vs tauEry1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tauEry1 - Red crested turaco - Tauraco erythrolophus SEQ2_DIR=/hive/data/genomes/tauEry1/tauEry1.2bit SEQ2_LEN=/hive/data/genomes/tauEry1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTauEry1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 479m16.276s cat fb.galGal6.chainTauEry1Link.txt # 891815531 bases of 1055588482 (84.485%) in intersection cat fb.galGal6.chainSynTauEry1Link.txt # 754044834 bases of 1055588482 (71.434%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TauEry1) > rbest.log 2>&1 & # real 315m40.917s cat fb.galGal6.chainRBest.TauEry1.txt # 810517802 bases of 1055588482 (76.784%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Tetraodon/tetNig2 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21 printf "# chicken vs Tetraodon # galGal6 vs tetNig2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tetNig2 - Tetraodon - Tetraodon nigroviridis SEQ2_DIR=/hive/data/genomes/tetNig2/tetNig2.2bit SEQ2_LEN=/hive/data/genomes/tetNig2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTetNig2.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 103m2.026s cat fb.galGal6.chainTetNig2Link.txt # 43782179 bases of 1055588482 (4.148%) in intersection cat fb.galGal6.chainSynTetNig2Link.txt # 10673340 bases of 1055588482 (1.011%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TetNig2) > rbest.log 2>&1 & # real 68m58.779s cat fb.galGal6.chainRBest.TetNig2.txt # 32928708 bases of 1055588482 (3.119%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Garter snake/thaSir1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21 printf "# chicken vs Garter snake # galGal6 vs thaSir1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: thaSir1 - Garter snake - Thamnophis sirtalis SEQ2_DIR=/hive/data/genomes/thaSir1/thaSir1.2bit SEQ2_LEN=/hive/data/genomes/thaSir1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzThaSir1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 263m16.804s cat fb.galGal6.chainThaSir1Link.txt # 124073447 bases of 1055588482 (11.754%) in intersection cat fb.galGal6.chainSynThaSir1Link.txt # 41632178 bases of 1055588482 (3.944%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 ThaSir1) > rbest.log 2>&1 & # real 179m29.254s cat fb.galGal6.chainRBest.ThaSir1.txt # 93424295 bases of 1055588482 (8.850%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Barn owl/tytAlb1 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21 printf "# chicken vs Barn owl # galGal6 vs tytAlb1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tytAlb1 - Barn owl - Tyto alba SEQ2_DIR=/hive/data/genomes/tytAlb1/tytAlb1.2bit SEQ2_LEN=/hive/data/genomes/tytAlb1/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzTytAlb1.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 510m12.860s cat fb.galGal6.chainTytAlb1Link.txt # 887980659 bases of 1055588482 (84.122%) in intersection cat fb.galGal6.chainSynTytAlb1Link.txt # 743212909 bases of 1055588482 (70.407%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 TytAlb1) > rbest.log 2>&1 & # real 302m9.764s cat fb.galGal6.chainRBest.TytAlb1.txt # 804558618 bases of 1055588482 (76.219%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs African clawed frog/xenLae2 - (DONE - 2018-10-21 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21 cd /hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21 printf "# chicken vs African clawed frog # galGal6 vs xenLae2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: xenLae2 - African clawed frog - Xenopus laevis SEQ2_DIR=/hive/data/genomes/xenLae2/xenLae2.2bit SEQ2_LEN=/hive/data/genomes/xenLae2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzXenLae2.2018-10-21 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 391m11.899s cat fb.galGal6.chainXenLae2Link.txt # 83674239 bases of 1055588482 (7.927%) in intersection cat fb.galGal6.chainSynXenLae2Link.txt # 40258327 bases of 1055588482 (3.814%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 XenLae2) > rbest.log 2>&1 & # real 242m24.342s cat fb.galGal6.chainRBest.XenLae2.txt # 69131006 bases of 1055588482 (6.549%) in intersection ############################################################################# # LASTZ chicken/galGal6 vs Japanese quail/cotJap2 - (DONE - 2018-10-25 - script/hiram) mkdir /hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25 cd /hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25 printf "# chicken vs Japanese quail # galGal6 vs cotJap2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_H=2000 BLASTZ_Y=3400 BLASTZ_L=4000 BLASTZ_K=2200 BLASTZ_M=254 BLASTZ_Q=/cluster/data/blastz/HoxD55.q # TARGET: galGal6 - chicken - Gallus gallus SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: cotJap2 - Japanese quail - Coturnix japonica SEQ2_DIR=/hive/data/genomes/cotJap2/cotJap2.2bit SEQ2_LEN=/hive/data/genomes/cotJap2/chrom.sizes SEQ2_CHUNK=1000000 SEQ2_LIMIT=2000 SEQ2_LAP=0 BASE=/hive/data/genomes/galGal6/bed/lastzCotJap2.2018-10-25 TMPDIR=/dev/shm " > DEF time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ -workhorse=hgwdev -bigClusterHub=ku \ -dbHost=hgwdev -smallClusterHub=ku \ -fileServer=hgwdev -syntenicNet) > do.log 2>&1 # real 402m14.191s cat fb.galGal6.chainCotJap2Link.txt # 950779519 bases of 1055588482 (90.071%) in intersection cat fb.galGal6.chainSynCotJap2Link.txt # 840595400 bases of 1055588482 (79.633%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ galGal6 CotJap2) > rbest.log 2>&1 & # real 331m41.351s cat fb.galGal6.chainRBest.CotJap2.txt # 846148712 bases of 1055588482 (80.159%) in intersection # running the swap mkdir /hive/data/genomes/cotJap2/bed/blastz.galGal6.swap cd /hive/data/genomes/cotJap2/bed/blastz.galGal6.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/galGal6/bed/lastzBosTau9.2018-10-25/DEF \ -swap -syntenicNet -workhorse=hgwdev \ -smallClusterHub=hgwdev-101 -bigClusterHub=ku \ ) > swap.log 2>&1 # real 286m17.880s cat fb.cotJap2.chainGalGal6Link.txt # 883933933 bases of 917263224 (96.366%) in intersection cat fb.cotJap2.chainSynGalGal6Link.txt # 838388062 bases of 917263224 (91.401%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` cotJap2 galGal6) > rbest.log 2>&1 & cat fb.cotJap2.chainRBest.GalGal6.txt # 846862875 bases of 917263224 (92.325%) in intersection ############################################################################# +# LASTZ chicken/galGal6 vs Zebrafish/danRer10 - (DONE - 2020-02-25 - script/hiram) + mkdir /hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25 + cd /hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25 + + printf "# chicken vs Zebrafish +# galGal6 vs danRer10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz +BLASTZ_H=2000 +BLASTZ_Y=3400 +BLASTZ_L=4000 +BLASTZ_K=2200 +BLASTZ_M=254 +BLASTZ_Q=/cluster/data/blastz/HoxD55.q + +# TARGET: galGal6 - chicken - Gallus gallus +SEQ1_DIR=/hive/data/genomes/galGal6/galGal6.2bit +SEQ1_LEN=/hive/data/genomes/galGal6/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: danRer10 - Zebrafish - Danio rerio +SEQ2_DIR=/hive/data/genomes/danRer10/danRer10.2bit +SEQ2_LEN=/hive/data/genomes/danRer10/chrom.sizes +SEQ2_CHUNK=1000000 +SEQ2_LIMIT=2000 +SEQ2_LAP=0 + +BASE=/hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25 +TMPDIR=/dev/shm +" > DEF + + time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \ + -workhorse=hgwdev -bigClusterHub=ku \ + -dbHost=hgwdev -smallClusterHub=ku \ + -fileServer=hgwdev -syntenicNet) > do.log 2>&1 + # real 156m19.439s + + cat fb.galGal6.chainDanRer10Link.txt + # 65140381 bases of 1055588482 (6.171%) in intersection + + cat fb.galGal6.chainSynDanRer10Link.txt + # 14892321 bases of 1055588482 (1.411%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + galGal6 danRer10) > rbest.log 2>&1 & + # real 181m30.518s + + cat fb.galGal6.chainRBest.DanRer10.txt + # 54759431 bases of 1055588482 (5.188%) in intersection + + mkdir /hive/data/genomes/danRer10/bed/blastz.galGal6.swap + cd /hive/data/genomes/danRer10/bed/blastz.galGal6.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/galGal6/bed/lastzDanRer10.2020-02-25/DEF \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet -swap) > swap.log 2>&1 & + # real 6m15.358s + + cat fb.danRer10.chainGalGal6Link.txt + # 80410462 bases of 1369683683 (5.871%) in intersection + cat fb.danRer10.chainSynGalGal6Link.txt + # 17599825 bases of 1369683683 (1.285%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + danRer10 galGal6) > rbest.log 2>&1 + # real 188m48.335s + + cat fb.danRer10.chainRBest.GalGal6.txt + # 55546117 bases of 1369683683 (4.055%) in intersection + +#############################################################################