7e0b08b36c5ad87458c4f8845c6dc4a67864e4ed lrnassar Mon Jun 10 10:05:56 2024 -0700 Adding latest liftOver run between genark and native DBS refs #33945 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index d644d42..ff68beb 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1,2716 +1,2803 @@ ############################################################################## # LASTZ tardigrades GCA_001949185.1 (DONE - 2021-10-06 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCA_001949185.1_Rvar_4.0 GCA_002082055.1_nHd_3.1 other other) \ > liftOverTest.log 2>&1 # check the total time grep -w real liftOverTest.log | tail -1 | sed -e 's/^/ # /;' # real 15m52.438s # this liftOverTest log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/liftOverTest.log ############################################################################## # LASTZ tardigrades GCA_001949185.1 vs. tardigrades GCA_002082055.1 # (DONE - 2021-10-06 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 cd /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 printf '# tardigrades GCA_002082055.1 vs. tardigrades GCA_001949185.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: tardigrades GCA_001949185.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tardigrades GCA_002082055.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCA_001949185.1_Rvar_4.0 -qAsmId GCA_002082055.1_nHd_3.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 10m31.512s sed -e 's/^/ # /;' fb.GCA_001949185.1.chainGCA_002082055.1Link.txt # 14450772 bases of 55842812 (25.878%) in intersection sed -e 's/^/ # /;' fb.GCA_001949185.1.chainSynGCA_002082055.1Link.txt # 6694962 bases of 55842812 (11.989%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt" \ GCA_001949185.1 GCA_002082055.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m39.278s sed -e 's/^/ # /;' fb.GCA_001949185.1.chainRBest.GCA_002082055.1.txt # 12952644 bases of 55842812 (23.195%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/002/082/055/GCA_002082055.1_nHd_3.1/trackData/blastz.GCA_001949185.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCA_001949185.1_Rvar_4.0 -qAsmId GCA_002082055.1_nHd_3.1 /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 2m1.276s sed -e 's/^/ # /;' fb.GCA_002082055.1.chainGCA_001949185.1Link.txt # 15159345 bases of 104154999 (14.555%) in intersection sed -e 's/^/ # /;' fb.GCA_002082055.1.chainSynGCA_001949185.1Link.txt # 7022280 bases of 104154999 (6.742%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt" \ GCA_002082055.1 GCA_001949185.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m39.919s sed -e 's/^/ # /;' fb.GCA_002082055.1.chainRBest.GCA_001949185.1.txt # 13053514 bases of 104154999 (12.533%) in intersection ############################################################################## # GCF_900094665.1_CAROLI_EIJ_v1.1 GCF_900095145.1_PAHARI_EIJ_v1.1 # (DONE - 2021-10-08 - Hiram) # to verify the sizes of the genomes to decide on target query # (this function could be folded into the pairLastz.sh script) # using the 'goto' shell function from Hiram's ~/.bashrc.hiram goto GCF_900094665.1 n50.pl *.sizes # reading: GCF_900094665.1_CAROLI_EIJ_v1.1.chrom.sizes # contig count: 3162, total size: 2553121441, one half size: 1276560720 # cumulative N50 count contig contig size 1253753066 8 chr5 145277780 1276560720 one half size 1376380316 9 chr10 122627250 goto GCF_900095145.1 n50.pl *.sizes # reading: GCF_900095145.1_PAHARI_EIJ_v1.1.chrom.sizes # contig count: 2581, total size: 2475012951, one half size: 1237506475 # cumulative N50 count contig contig size 1192339185 8 chr7 113323912 1237506475 one half size 1303745413 9 chr8 111406228 # in this case, choosing the larger genome GCF_900094665.1_CAROLI_EIJ_v1.1 # as target cd /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs # the single command to run everything: time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_900094665.1_CAROLI_EIJ_v1.1 \ GCF_900095145.1_PAHARI_EIJ_v1.1 mammal mammal) >> mice.lastz.log 2>&1 & # copy of makeDoc from /hive/data/genomes/asmHubs/refseqBuild/GCF/900/094/665/GCF_900094665.1_CAROLI_EIJ_v1.1/trackData/lastzGCF_900095145.1.2021-10-08/makeDoc.txt ############################################################################## # LASTZ Ryukyu mouse GCF_900094665.1 vs. shrew mouse GCF_900095145.1 # (DONE - 2021-10-08 - hiram) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/900/094/665/GCF_900094665.1_CAROLI_EIJ_v1.1/trackData/lastzGCF_900095145.1.2021-10-08 cd /hive/data/genomes/asmHubs/allBuild/GCF/900/094/665/GCF_900094665.1_CAROLI_EIJ_v1.1/trackData/lastzGCF_900095145.1.2021-10-08 printf '# shrew mouse GCF_900095145.1 vs. Ryukyu mouse GCF_900094665.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Ryukyu mouse GCF_900094665.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: shrew mouse GCF_900095145.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/900/094/665/GCF_900094665.1_CAROLI_EIJ_v1.1/trackData/lastzGCF_900095145.1.2021-10-08 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_900094665.1_CAROLI_EIJ_v1.1 -qAsmId GCF_900095145.1_PAHARI_EIJ_v1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 547m27.209s sed -e 's/^/ # /;' fb.GCF_900094665.1.chainGCF_900095145.1Link.txt # 2044833501 bases of 2553121441 (80.092%) in intersection sed -e 's/^/ # /;' fb.GCF_900094665.1.chainSynGCF_900095145.1Link.txt # 1909243125 bases of 2553121441 (74.781%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.chrom.sizes.txt" \ GCF_900094665.1 GCF_900095145.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 844m36.808s sed -e 's/^/ # /;' fb.GCF_900094665.1.chainRBest.GCF_900095145.1.txt # 1922295923 bases of 2553121441 (75.292%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/900/095/145/GCF_900095145.1_PAHARI_EIJ_v1.1/trackData/blastz.GCF_900094665.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_900094665.1_CAROLI_EIJ_v1.1 -qAsmId GCF_900095145.1_PAHARI_EIJ_v1.1 /hive/data/genomes/asmHubs/allBuild/GCF/900/094/665/GCF_900094665.1_CAROLI_EIJ_v1.1/trackData/lastzGCF_900095145.1.2021-10-08/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 284m47.765s sed -e 's/^/ # /;' fb.GCF_900095145.1.chainGCF_900094665.1Link.txt # 2030243186 bases of 2475012951 (82.030%) in intersection sed -e 's/^/ # /;' fb.GCF_900095145.1.chainSynGCF_900094665.1Link.txt # 1904468244 bases of 2475012951 (76.948%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/900/094/665/GCF_900094665.1/GCF_900094665.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/900/095/145/GCF_900095145.1/GCF_900095145.1.chrom.sizes.txt" \ GCF_900095145.1 GCF_900094665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 798m20.989s sed -e 's/^/ # /;' fb.GCF_900095145.1.chainRBest.GCF_900094665.1.txt # 1922376371 bases of 2475012951 (77.671%) in intersection ############################################################################## # GCF_000413155.1_DPV01 GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p # (DONE - 2021-10-08 - Hiram) # to verify the sizes of the genomes to decide on target query # (this function could be folded into the pairLastz.sh script) # using the 'goto' shell function from Hiram's ~/.bashrc.hiram goto GCF_000413155.1 n50.pl *.sizes n50.pl *.sizes # reading: GCF_000413155.1_DPV01.chrom.sizes # contig count: 80317, total size: 556480649, one half size: 278240324 # cumulative N50 count contig contig size 278069349 324 NW_008246829.1 335344 278240324 one half size 278404638 325 NW_008246830.1 335289 goto GCF_009389715.1 n50.pl *.sizes # reading: GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p.chrom.sizes # contig count: 2391, total size: 773189301, one half size: 386594650 # cumulative N50 count contig contig size 385590432 18 NC_052409.1 9812533 386594650 one half size 390318775 19 NW_024067666.1 4728343 # in this case, choosing the larger genome # GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p # as target and GCF_000413155.1_DPV01 as query cd /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs # the single command to run everything: time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p \ GCF_000413155.1_DPV01 other other) >> datePalm.lastz.log 2>&1 & # real 585m49.200s # user 0m3.435s # sys 0m6.165s ############################################################################## # LASTZ date palm GCF_009389715.1 vs. date palm GCF_000413155.1 (DONE - 2021-10-18 - hiram) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/009/389/715/GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p/trackData/lastzGCF_000413155.1.2021-10-18 cd /hive/data/genomes/asmHubs/allBuild/GCF/009/389/715/GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p/trackData/lastzGCF_000413155.1.2021-10-18 printf '# date palm GCF_000413155.1 vs. date palm GCF_009389715.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: date palm GCF_009389715.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: date palm GCF_000413155.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=500 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/009/389/715/GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p/trackData/lastzGCF_000413155.1.2021-10-18 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p -qAsmId GCF_000413155.1_DPV01 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 316m4.783s sed -e 's/^/ # /;' fb.GCF_009389715.1.chainGCF_000413155.1Link.txt # 611238317 bases of 773189301 (79.054%) in intersection sed -e 's/^/ # /;' fb.GCF_009389715.1.chainSynGCF_000413155.1Link.txt # 426120778 bases of 773189301 (55.112%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.chrom.sizes.txt" \ GCF_009389715.1 GCF_000413155.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 18m42.901s sed -e 's/^/ # /;' fb.GCF_009389715.1.chainRBest.GCF_000413155.1.txt # 394043180 bases of 773189301 (50.963%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/413/155/GCF_000413155.1_DPV01/trackData/blastz.GCF_009389715.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p -qAsmId GCF_000413155.1_DPV01 /hive/data/genomes/asmHubs/allBuild/GCF/009/389/715/GCF_009389715.1_palm_55x_up_171113_PBpolish2nd_filt_p/trackData/lastzGCF_000413155.1.2021-10-18/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 217m53.130s sed -e 's/^/ # /;' fb.GCF_000413155.1.chainGCF_009389715.1Link.txt # 470755615 bases of 556480649 (84.595%) in intersection sed -e 's/^/ # /;' fb.GCF_000413155.1.chainSynGCF_009389715.1Link.txt # 386385047 bases of 556480649 (69.434%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.chrom.sizes.txt" \ GCF_000413155.1 GCF_009389715.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 33m7.581s sed -e 's/^/ # /;' fb.GCF_000413155.1.chainRBest.GCF_009389715.1.txt # 430390896 bases of 556480649 (77.342%) in intersection ############################################################################## time (~/kent/src/hg/utils/automation/pairLastz.sh \ hg38 GCF_000349665.1_MesAur1.0 primate mammal) >> goldenHamster.lastz.log 2>&1 & # real 1326m29.271s # user 0m1.945s # sys 0m2.347s ############################################################################## # LASTZ Human Hg38 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Human Hg38 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Human Hg38 SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 816m1.961s sed -e 's/^/ # /;' fb.hg38.chainGCF_000349665.1Link.txt # 927958037 bases of 3272116950 (28.360%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCF_000349665.1Link.txt # 849347972 bases of 3272116950 (25.957%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ hg38 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 227m0.804s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_000349665.1.txt # 840160627 bases of 3272116950 (25.676%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 66m26.977s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainHg38Link.txt # 864739427 bases of 2504925039 (34.522%) in intersection sed -e 's/^/ # /;' fb.GCF_000349665.1.chainSynHg38Link.txt # 812701606 bases of 2504925039 (32.444%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ GCF_000349665.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 216m58.998s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRBest.Hg38.txt # 841788407 bases of 2504925039 (33.605%) in intersection ############################################################################## # LASTZ Mouse Mm10 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Mouse Mm10 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 822m9.572s sed -e 's/^/ # /;' fb.mm10.chainGCF_000349665.1Link.txt # 1517320069 bases of 2818974548 (53.825%) in intersection sed -e 's/^/ # /;' fb.mm10.chainSynGCF_000349665.1Link.txt # 1368250969 bases of 2818974548 (48.537%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ mm10 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 457m57.111s sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_000349665.1.txt # 1350867428 bases of 2818974548 (47.921%) in intersection ### and for the swap # swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap # running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap/runSwap.sh ############################################################################## # LASTZ Mouse Mm10 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Mouse Mm10 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 822m9.572s sed -e 's/^/ # /;' fb.mm10.chainGCF_000349665.1Link.txt # 1517320069 bases of 2818974548 (53.825%) in intersection sed -e 's/^/ # /;' fb.mm10.chainSynGCF_000349665.1Link.txt # 1368250969 bases of 2818974548 (48.537%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ mm10 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 457m57.111s sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_000349665.1.txt # 1350867428 bases of 2818974548 (47.921%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 101m40.814s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainMm10Link.txt # 1420756145 bases of 2504925039 (56.719%) in intersection sed -e 's/^/ # /;' fb.GCF_000349665.1.chainSynMm10Link.txt # 1317050872 bases of 2504925039 (52.578%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ GCF_000349665.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 429m34.320s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRBest.Mm10.txt # 1352697681 bases of 2504925039 (54.002%) in intersection real 1811m22.412s user 0m2.184s sys 0m3.047s ############################################################################## # LASTZ Mouse Mm39 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Mouse Mm39 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 827m23.676s sed -e 's/^/ # /;' fb.mm39.chainGCF_000349665.1Link.txt # 1471502725 bases of 2728222451 (53.936%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCF_000349665.1Link.txt # 1328672778 bases of 2728222451 (48.701%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ mm39 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 477m51.437s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_000349665.1.txt # 1352204504 bases of 2728222451 (49.564%) in intersection ### and for the swap # swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap # running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap/runSwap.sh ############################################################################## # LASTZ Mouse Mm39 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Mouse Mm39 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 827m23.676s sed -e 's/^/ # /;' fb.mm39.chainGCF_000349665.1Link.txt # 1471502725 bases of 2728222451 (53.936%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCF_000349665.1Link.txt # 1328672778 bases of 2728222451 (48.701%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ mm39 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 477m51.437s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_000349665.1.txt # 1352204504 bases of 2728222451 (49.564%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 101m49.459s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainMm39Link.txt # 1419668050 bases of 2504925039 (56.675%) in intersection sed -e 's/^/ # /;' fb.GCF_000349665.1.chainSynMm39Link.txt # 1318426965 bases of 2504925039 (52.633%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ GCF_000349665.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 449m50.789s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRBest.Mm39.txt # 1354030653 bases of 2504925039 (54.055%) in intersection real 1856m55.873s user 0m2.166s sys 0m3.097s ############################################################################## # LASTZ Rat Rn6 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Rat Rn6 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Rat Rn6 SEQ1_DIR=/hive/data/genomes/rn6/rn6.2bit SEQ1_LEN=/hive/data/genomes/rn6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 825m37.498s sed -e 's/^/ # /;' fb.rn6.chainGCF_000349665.1Link.txt # 1514418886 bases of 2870182909 (52.764%) in intersection sed -e 's/^/ # /;' fb.rn6.chainSynGCF_000349665.1Link.txt # 1362599174 bases of 2870182909 (47.474%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ rn6 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 573m22.505s sed -e 's/^/ # /;' fb.rn6.chainRBest.GCF_000349665.1.txt # 1350327568 bases of 2870182909 (47.047%) in intersection ### and for the swap # swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap # running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap/runSwap.sh ############################################################################## # LASTZ Rat Rn6 vs. golden hamster GCF_000349665.1 # (DONE - 2021-10-19 - hiram) mkdir /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 cd /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 printf '# golden hamster GCF_000349665.1 vs. Rat Rn6 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Rat Rn6 SEQ1_DIR=/hive/data/genomes/rn6/rn6.2bit SEQ1_LEN=/hive/data/genomes/rn6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster GCF_000349665.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 825m37.498s sed -e 's/^/ # /;' fb.rn6.chainGCF_000349665.1Link.txt # 1514418886 bases of 2870182909 (52.764%) in intersection sed -e 's/^/ # /;' fb.rn6.chainSynGCF_000349665.1Link.txt # 1362599174 bases of 2870182909 (47.474%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ rn6 GCF_000349665.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 573m22.505s sed -e 's/^/ # /;' fb.rn6.chainRBest.GCF_000349665.1.txt # 1350327568 bases of 2870182909 (47.047%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 101m35.604s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRn6Link.txt # 1413849889 bases of 2504925039 (56.443%) in intersection sed -e 's/^/ # /;' fb.GCF_000349665.1.chainSynRn6Link.txt # 1311578944 bases of 2504925039 (52.360%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \ GCF_000349665.1 rn6) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 488m35.716s sed -e 's/^/ # /;' fb.GCF_000349665.1.chainRBest.Rn6.txt # 1350825251 bases of 2504925039 (53.927%) in intersection real 1989m11.755s user 0m1.959s sys 0m2.860s ############################################################################## # LASTZ sheep GCF_002742125.1 vs. Sheep OviAri4 (DONE- 2021-11-08 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_002742125.1_Oar_rambouillet_v1.0 oviAri4 mammal mammal) \ > sheepLiftOver_20211108.log 2>&1 & # check the total time grep -w real sheepLiftOver_20211108.log | tail -1 | sed -e 's/^/ # /;' # real 2380m46.742s # this sheepLiftOver_20211108 log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/sheepLiftOver_20211108.log ############################################################################## # LASTZ sheep GCF_002742125.1 vs. Sheep OviAri4 # (DONE - 2021-11-08 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 printf '# Sheep OviAri4 vs. sheep GCF_002742125.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep GCF_002742125.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Sheep OviAri4 SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1306m58.735s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainOviAri4Link.txt # 2751767534 bases of 2869914396 (95.883%) in intersection sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynOviAri4Link.txt # 2683354898 bases of 2869914396 (93.499%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ \ GCF_002742125.1 oviAri4) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 134m53.482s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.OviAri4.txt # 2516745591 bases of 2869914396 (87.694%) in intersection ### and for the swap cd /hive/data/genomes/oviAri4/bed/blastz.GCF_002742125.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzOviAri4.2021-11-08/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 813m49.535s sed -e 's/^/ # /;' fb.oviAri4.chainGCF_002742125.1Link.txt # 2554085476 bases of 2615516299 (97.651%) in intersection sed -e 's/^/ # /;' fb.oviAri4.chainSynGCF_002742125.1Link.txt # 2527079442 bases of 2615516299 (96.619%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ \ oviAri4 GCF_002742125.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 125m4.180s sed -e 's/^/ # /;' fb.oviAri4.chainRBest.GCF_002742125.1.txt # 2520434078 bases of 2615516299 (96.365%) in intersection real 2380m46.742s user 0m1.784s sys 0m1.912s ############################################################################## # LASTZ sheep GCF_016772045.1 vs. Sheep OviAri3 (DONE - 2021-12-15 -Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_016772045.1_ARS-UI_Ramb_v2.0 oviAri3 mammal mammal) \ > GCF016772045_oviAri3_20211215.log 2>&1 & # check the total time grep -w real GCF016772045_oviAri3_20211215.log | tail -1 | sed -e 's/^/ # /;' # real 2508m50.449s # this GCF016772045_oviAri3_20211215.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15//makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCF016772045_oviAri3_20211215.log ############################################################################## # LASTZ sheep GCF_016772045.1 vs. Sheep OviAri3 # (DONE - 2021-12-15 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 printf '# Sheep OviAri3 vs. sheep GCF_016772045.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep GCF_016772045.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Sheep OviAri3 SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.2bit SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1573m35.149s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainOviAri3Link.txt # 2511613301 bases of 2628146905 (95.566%) in intersection sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynOviAri3Link.txt # 2472798897 bases of 2628146905 (94.089%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ \ GCF_016772045.1 oviAri3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 103m6.701s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.OviAri3.txt # 2466641987 bases of 2628146905 (93.855%) in intersection ### and for the swap cd /hive/data/genomes/oviAri3/bed/blastz.GCF_016772045.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri3.2021-12-15/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 709m20.158s sed -e 's/^/ # /;' fb.oviAri3.chainGCF_016772045.1Link.txt # 2499875349 bases of 2619054388 (95.450%) in intersection sed -e 's/^/ # /;' fb.oviAri3.chainSynGCF_016772045.1Link.txt # 2475599907 bases of 2619054388 (94.523%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ \ oviAri3 GCF_016772045.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 122m47.847s sed -e 's/^/ # /;' fb.oviAri3.chainRBest.GCF_016772045.1.txt # 2470367813 bases of 2619054388 (94.323%) in intersection real 2508m50.449s user 0m1.587s sys 0m1.678s ############################################################################## # LASTZ sheep GCF_016772045.1 vs. Sheep OviAri4 (DONE - 2021-12-15 -Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_016772045.1_ARS-UI_Ramb_v2.0 oviAri4 mammal mammal) \ > GCF016772045_oviAri4_20211215.log 2>&1 & # check the total time grep -w real GCF016772045_oviAri4_20211215.log | tail -1 | sed -e 's/^/ # /;' # real 2669m31.448s # this GCF016772045_oviAri4_20211215.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15//makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCF016772045_oviAri4_20211215.log ############################################################################## # LASTZ sheep GCF_016772045.1 vs. Sheep OviAri4 # (DONE - 2021-12-15 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 printf '# Sheep OviAri4 vs. sheep GCF_016772045.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep GCF_016772045.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Sheep OviAri4 SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1657m21.821s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainOviAri4Link.txt # 2552765241 bases of 2628146905 (97.132%) in intersection sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynOviAri4Link.txt # 2521297402 bases of 2628146905 (95.934%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ \ GCF_016772045.1 oviAri4) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 110m56.360s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.OviAri4.txt # 2512287192 bases of 2628146905 (95.592%) in intersection ### and for the swap cd /hive/data/genomes/oviAri4/bed/blastz.GCF_016772045.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/lastzOviAri4.2021-12-15/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 777m47.304s sed -e 's/^/ # /;' fb.oviAri4.chainGCF_016772045.1Link.txt # 2551757085 bases of 2615516299 (97.562%) in intersection sed -e 's/^/ # /;' fb.oviAri4.chainSynGCF_016772045.1Link.txt # 2526678124 bases of 2615516299 (96.603%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ \ oviAri4 GCF_016772045.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 123m25.562s sed -e 's/^/ # /;' fb.oviAri4.chainRBest.GCF_016772045.1.txt # 2516185710 bases of 2615516299 (96.202%) in intersection real 2669m31.448s user 0m1.595s sys 0m1.620s ############################################################################## # LASTZ sheep GCF_002742125.1 vs. sheep GCF_016772045.1 (DONE - 2021-12-15 -Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_002742125.1_Oar_rambouillet_v1.0 GCF_016772045.1_ARS-UI_Ramb_v2.0 mammal mammal) \ > GCF002742125_GCF016772045_20211215.log 2>&1 & # check the total time grep -w real GCF002742125_GCF016772045_20211215.log | tail -1 | sed -e 's/^/ # /;' # real 2656m30.586s # this GCF002742125_GCF016772045_20211215.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCF002742125_GCF016772045_20211215.log ############################################################################## # LASTZ sheep GCF_002742125.1 vs. sheep GCF_016772045.1 # (DONE - 2021-12-15 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15 cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15 printf '# sheep GCF_016772045.1 vs. sheep GCF_002742125.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep GCF_002742125.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: sheep GCF_016772045.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -qAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1439m18.311s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainGCF_016772045.1Link.txt # 2838492016 bases of 2869914396 (98.905%) in intersection sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynGCF_016772045.1Link.txt # 2803625709 bases of 2869914396 (97.690%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ GCF_002742125.1 GCF_016772045.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 88m6.029s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.GCF_016772045.1.txt # 2614623978 bases of 2869914396 (91.105%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/blastz.GCF_002742125.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -qAsmId GCF_016772045.1_ARS-UI_Ramb_v2.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzGCF_016772045.1.2021-12-15/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 1047m12.920s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainGCF_002742125.1Link.txt # 2622530937 bases of 2628146905 (99.786%) in intersection sed -e 's/^/ # /;' fb.GCF_016772045.1.chainSynGCF_002742125.1Link.txt # 2612741995 bases of 2628146905 (99.414%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ GCF_016772045.1 GCF_002742125.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m52.743s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.GCF_002742125.1.txt # 2611860239 bases of 2628146905 (99.380%) in intersection real 2656m30.586s user 0m1.556s sys 0m1.520s ############################################################################## # LASTZ sheep GCF_002742125.1 vs. Mouse Mm39 (DONE - 2021-12-21 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_002742125.1_Oar_rambouillet_v1.0 mm39 mammal mammal) \ > GCF002742125_mm39_20211221.log 2>&1 & # check the total time grep -w real GCF002742125_mm39_20211221.log | tail -1 | sed -e 's/^/ # /;' # real 1011m49.661s # this GCF002742125_mm39_20211221.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21/makeDoc.txt # this command outputs this makeDoc text: cat ~/kent/src/hg/utils/automation/GCF002742125_mm39_20211221.log ############################################################################## # LASTZ sheep GCF_002742125.1 vs. Mouse Mm39 # (DONE - 2021-12-21 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 printf '# Mouse Mm39 vs. sheep GCF_002742125.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep GCF_002742125.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Mouse Mm39 SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 230m6.460s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainMm39Link.txt # 724687034 bases of 2869914396 (25.251%) in intersection sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynMm39Link.txt # 661688482 bases of 2869914396 (23.056%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ \ GCF_002742125.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 362m25.103s sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.Mm39.txt # 660762547 bases of 2869914396 (23.024%) in intersection ### and for the swap cd /hive/data/genomes/mm39/bed/blastz.GCF_002742125.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 92m24.630s sed -e 's/^/ # /;' fb.mm39.chainGCF_002742125.1Link.txt # 695954726 bases of 2728222451 (25.509%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCF_002742125.1Link.txt # 646953218 bases of 2728222451 (23.713%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ \ mm39 GCF_002742125.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 326m52.826s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_002742125.1.txt # 660752248 bases of 2728222451 (24.219%) in intersection real 1011m49.661s user 0m1.668s sys 0m1.378s ############################################################################## # LASTZ dog GCF_014441545.1 vs. Dog CanFam3 (DONE - 2022-01-13 -Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_014441545.1_ROS_Cfam_1.0 canFam3 mammal mammal) \ > GCF014441545_canFam3_20220113.log 2>&1 & # check the total time grep -w real GCF014441545_canFam3_20220113.log | tail -1 | sed -e 's/^/ # /;' # real 758m9.174s # this GCF014441545_canFam3_20220113.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the dog GCF_014441545.1 assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCF014441545_canFam3_20220113.log ############################################################################## # LASTZ dog GCF_014441545.1 vs. Dog CanFam3 # (DONE - 2022-01-13 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 cd /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 printf '# Dog CanFam3 vs. dog GCF_014441545.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: dog GCF_014441545.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Dog CanFam3 SEQ2_DIR=/hive/data/genomes/canFam3/canFam3.2bit SEQ2_LEN=/hive/data/genomes/canFam3/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_014441545.1_ROS_Cfam_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 436m5.199s sed -e 's/^/ # /;' fb.GCF_014441545.1.chainCanFam3Link.txt # 2352312522 bases of 2396858295 (98.141%) in intersection sed -e 's/^/ # /;' fb.GCF_014441545.1.chainSynCanFam3Link.txt # 2343016231 bases of 2396858295 (97.754%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ \ GCF_014441545.1 canFam3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 70m5.098s sed -e 's/^/ # /;' fb.GCF_014441545.1.chainRBest.CanFam3.txt # 2305842969 bases of 2396858295 (96.203%) in intersection ### and for the swap cd /hive/data/genomes/canFam3/bed/blastz.GCF_014441545.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_014441545.1_ROS_Cfam_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 185m43.935s sed -e 's/^/ # /;' fb.canFam3.chainGCF_014441545.1Link.txt # 2355576959 bases of 2410976875 (97.702%) in intersection sed -e 's/^/ # /;' fb.canFam3.chainSynGCF_014441545.1Link.txt # 2335796753 bases of 2410976875 (96.882%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ \ canFam3 GCF_014441545.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 66m14.435s sed -e 's/^/ # /;' fb.canFam3.chainRBest.GCF_014441545.1.txt # 2307013600 bases of 2410976875 (95.688%) in intersection ############################################################################## real 758m9.174s user 0m1.449s sys 0m1.346s ############################################################################## # LASTZ mummichog GCF_011125445.2 vs. mummichog GCF_000826765.1 (DONE - 2022-01-21 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCF_011125445.2_MU-UCD_Fhet_4.1 GCF_000826765.1_Fundulus_heteroclitus-3.0.2 other other) \ > GCF011125445_GCF000826765_20220121.log 2>&1 & # check the total time grep -w real GCF011125445_GCF000826765_20220121.log | tail -1 | sed -e 's/^/ # /;' # real 1621m36.194s # this GCF011125445_GCF000826765_20220121.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCF011125445_GCF000826765_20220121.log ############################################################################## # LASTZ mummichog GCF_011125445.2 vs. mummichog GCF_000826765.1 # (DONE - 2022-01-21 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 cd /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 printf '# mummichog GCF_000826765.1 vs. mummichog GCF_011125445.2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: mummichog GCF_011125445.2 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: mummichog GCF_000826765.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_011125445.2_MU-UCD_Fhet_4.1 -qAsmId GCF_000826765.1_Fundulus_heteroclitus-3.0.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 755m29.866s sed -e 's/^/ # /;' fb.GCF_011125445.2.chainGCF_000826765.1Link.txt # 1069310182 bases of 1203505739 (88.850%) in intersection sed -e 's/^/ # /;' fb.GCF_011125445.2.chainSynGCF_000826765.1Link.txt # 885838715 bases of 1203505739 (73.605%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt" \ GCF_011125445.2 GCF_000826765.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 86m1.406s sed -e 's/^/ # /;' fb.GCF_011125445.2.chainRBest.GCF_000826765.1.txt # 858755159 bases of 1203505739 (71.354%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/826/765/GCF_000826765.1_Fundulus_heteroclitus-3.0.2/trackData/blastz.GCF_011125445.2.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_011125445.2_MU-UCD_Fhet_4.1 -qAsmId GCF_000826765.1_Fundulus_heteroclitus-3.0.2 /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 706m8.827s sed -e 's/^/ # /;' fb.GCF_000826765.1.chainGCF_011125445.2Link.txt # 906492141 bases of 1021898560 (88.707%) in intersection sed -e 's/^/ # /;' fb.GCF_000826765.1.chainSynGCF_011125445.2Link.txt # 852990578 bases of 1021898560 (83.471%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt" \ GCF_000826765.1 GCF_011125445.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 73m55.254s sed -e 's/^/ # /;' fb.GCF_000826765.1.chainRBest.GCF_011125445.2.txt # 865608764 bases of 1021898560 (84.706%) in intersection ############################################################################## real 1621m36.194s user 0m2.046s sys 0m2.922s ############################################################################## # LASTZ kinetoplastids GCA_000340355.2 vs. kinetoplastids GCF_000002845.2 (DONE - 2022-02-06 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6 GCF_000002845.2_ASM284v2 other other) \ > GCA_000340355_GCF_000002845_20220204.log 2>&1 & # check the total time grep -w real GCA_000340355_GCF_000002845_20220204.log | tail -1 | sed -e 's/^/ # /;' # real 27m14.153s # this GCA_000340355_GCF_000002845_20220204.log log file happens to have a copy of the make doc, as well # as the copy of the make doc left in the target assembly directory: # /hive/data/genomes/asmHubs/allBuild/GCA/000/340/355/GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6/trackData/lastzGCF_000002845.2.2022-02-06/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/GCA_000340355_GCF_000002845_20220204.log ############################################################################## # LASTZ kinetoplastids GCA_000340355.2 vs. kinetoplastids GCF_000002845.2 # (DONE - 2022-02-06 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCA/000/340/355/GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6/trackData/lastzGCF_000002845.2.2022-02-06 cd /hive/data/genomes/asmHubs/allBuild/GCA/000/340/355/GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6/trackData/lastzGCF_000002845.2.2022-02-06 printf '# kinetoplastids GCF_000002845.2 vs. kinetoplastids GCA_000340355.2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: kinetoplastids GCA_000340355.2 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: kinetoplastids GCF_000002845.2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCA/000/340/355/GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6/trackData/lastzGCF_000002845.2.2022-02-06 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6 -qAsmId GCF_000002845.2_ASM284v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 21m44.561s sed -e 's/^/ # /;' fb.GCA_000340355.2.chainGCF_000002845.2Link.txt # 31699291 bases of 35210150 (90.029%) in intersection sed -e 's/^/ # /;' fb.GCA_000340355.2.chainSynGCF_000002845.2Link.txt # 30406396 bases of 35210150 (86.357%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.chrom.sizes.txt" \ GCA_000340355.2 GCF_000002845.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m2.843s sed -e 's/^/ # /;' fb.GCA_000340355.2.chainRBest.GCF_000002845.2.txt # 30393628 bases of 35210150 (86.321%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/002/845/GCF_000002845.2_ASM284v2/trackData/blastz.GCA_000340355.2.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6 -qAsmId GCF_000002845.2_ASM284v2 /hive/data/genomes/asmHubs/allBuild/GCA/000/340/355/GCA_000340355.2_Leishmania_braziliensis_M2903-1.0.6/trackData/lastzGCF_000002845.2.2022-02-06/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 3m24.068s sed -e 's/^/ # /;' fb.GCF_000002845.2.chainGCA_000340355.2Link.txt # 31582268 bases of 32068771 (98.483%) in intersection sed -e 's/^/ # /;' fb.GCF_000002845.2.chainSynGCA_000340355.2Link.txt # 30612946 bases of 32068771 (95.460%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/000/340/355/GCA_000340355.2/GCA_000340355.2.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.chrom.sizes.txt" \ GCF_000002845.2 GCA_000340355.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m2.112s sed -e 's/^/ # /;' fb.GCF_000002845.2.chainRBest.GCA_000340355.2.txt # 30310385 bases of 32068771 (94.517%) in intersection ############################################################################## real 27m14.153s user 0m1.233s sys 0m1.147s ############################################################################# # LASTZ water buffalo GCF_003121395.1 vs. Cow BosTau9 (DONE - 2022-01-17) ./pairLastz.sh GCF_003121395.1_ASM312139v1 bosTau9 mammal mammal # this command outputs this makeDoc text: cat /hive/data/genomes/asmHubs/refseqBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15/makeDoc.txt ############################################################################## # LASTZ water buffalo GCF_003121395.1 vs. Cow BosTau9 # (DONE - 2022-03-21 - hiram) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 cd /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 printf '# Cow BosTau9 vs. water buffalo GCF_003121395.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: water buffalo GCF_003121395.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Cow BosTau9 SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_003121395.1_ASM312139v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 586m13.240s sed -e 's/^/ # /;' fb.GCF_003121395.1.chainBosTau9Link.txt # 2530022888 bases of 2655780776 (95.265%) in intersection sed -e 's/^/ # /;' fb.GCF_003121395.1.chainSynBosTau9Link.txt # 2503488174 bases of 2655780776 (94.266%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt" \ \ GCF_003121395.1 bosTau9) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 131m51.569s sed -e 's/^/ # /;' fb.GCF_003121395.1.chainRBest.BosTau9.txt # 2481923005 bases of 2655780776 (93.454%) in intersection ### and for the swap cd /hive/data/genomes/bosTau9/bed/blastz.GCF_003121395.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_003121395.1_ASM312139v1 /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 217m58.432s sed -e 's/^/ # /;' fb.bosTau9.chainGCF_003121395.1Link.txt # 2545585532 bases of 2715853792 (93.731%) in intersection sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_003121395.1Link.txt # 2515328392 bases of 2715853792 (92.616%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt" \ \ bosTau9 GCF_003121395.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 142m40.163s sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_003121395.1.txt # 2481700410 bases of 2715853792 (91.378%) in intersection ############################################################################## # LASTZ crab-eating macaque GCF_012559485.2 vs. chimpanzee GCF_002880755.1 # (DONE - 2022-05-24 - Jairo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzGCF_002880755.1.2022-05-24 cd /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzGCF_002880755.1.2022-05-24 printf '# chimpanzee GCF_002880755.1 vs. crab-eating macaque GCF_012559485.2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_T=2 BLASTZ_O=600 BLASTZ_E=150 BLASTZ_M=254 BLASTZ_K=4500 BLASTZ_Y=15000 BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q # A C G T # A 90 -330 -236 -356 # C -330 100 -318 -236 # G -236 -318 100 -330 # T -356 -236 -330 90 # TARGET: crab-eating macaque 2021-10-26 GCF_012559485.2_MFA1912RKSv2 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: chimpanzee 2018-01-19 GCF_002880755.1_Clint_PTRv2 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzGCF_002880755.1.2022-05-24 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_012559485.2_MFA1912RKSv2 -qAsmId GCF_002880755.1_Clint_PTRv2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1248m33.272s sed -e 's/^/ # /;' fb.GCF_012559485.2.chainGCF_002880755.1Link.txt # 2431892897 bases of 2800899072 (86.825%) in intersection sed -e 's/^/ # /;' fb.GCF_012559485.2.chainSynGCF_002880755.1Link.txt # 2415493420 bases of 2800899072 (86.240%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.chrom.sizes.txt" \ GCF_012559485.2 GCF_002880755.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 145m11.563s sed -e 's/^/ # /;' fb.GCF_012559485.2.chainRBest.GCF_002880755.1.txt # 2408578083 bases of 2800899072 (85.993%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/002/880/755/GCF_002880755.1_Clint_PTRv2/trackData/blastz.GCF_012559485.2.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_012559485.2_MFA1912RKSv2 -qAsmId GCF_002880755.1_Clint_PTRv2 /hive/data/genomes/asmHubs/allBuild/GCF/012/559/485/GCF_012559485.2_MFA1912RKSv2/trackData/lastzGCF_002880755.1.2022-05-24/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 106m38.656s sed -e 's/^/ # /;' fb.GCF_002880755.1.chainGCF_012559485.2Link.txt # 2490856583 bases of 3050398082 (81.657%) in intersection sed -e 's/^/ # /;' fb.GCF_002880755.1.chainSynGCF_012559485.2Link.txt # 2466586935 bases of 3050398082 (80.861%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.chrom.sizes.txt" \ GCF_002880755.1 GCF_012559485.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 146m55.957s sed -e 's/^/ # /;' fb.GCF_002880755.1.chainRBest.GCF_012559485.2.txt # 2408485685 bases of 3050398082 (78.956%) in intersection ############################################################################## # LASTZ platypus GCF_004115215.2 vs. platypus GCA_002966995.1 # (DONE - 2022-07-18 - hiram) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 cd /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 printf '# platypus GCA_002966995.1 vs. platypus GCF_004115215.2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: platypus 2020-11-06 GCF_004115215.2_mOrnAna1.pri.v4 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: platypus 2018-03-02 GCA_002966995.1_ASM296699v1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_004115215.2_mOrnAna1.pri.v4 -qAsmId GCA_002966995.1_ASM296699v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' sed -e 's/^/ # /;' fb.GCF_004115215.2.chainGCA_002966995.1Link.txt # 1833760395 bases of 1859281927 (98.627%) in intersection sed -e 's/^/ # /;' fb.GCF_004115215.2.chainSynGCA_002966995.1Link.txt # 1822260569 bases of 1859281927 (98.009%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt" \ GCF_004115215.2 GCA_002966995.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' sed -e 's/^/ # /;' fb.GCF_004115215.2.chainRBest.GCA_002966995.1.txt ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/002/966/995/GCA_002966995.1_ASM296699v1/trackData/blastz.GCF_004115215.2.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_004115215.2_mOrnAna1.pri.v4 -qAsmId GCA_002966995.1_ASM296699v1 /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 505m1.293s sed -e 's/^/ # /;' fb.GCA_002966995.1.chainGCF_004115215.2Link.txt # 1968124670 bases of 1990409179 (98.880%) in intersection sed -e 's/^/ # /;' fb.GCA_002966995.1.chainSynGCF_004115215.2Link.txt # 1943307833 bases of 1990409179 (97.634%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt" \ GCA_002966995.1 GCF_004115215.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 44m40.845s sed -e 's/^/ # /;' fb.GCA_002966995.1.chainRBest.GCF_004115215.2.txt # 1816571806 bases of 1990409179 (91.266%) in intersection ############################################################################## # LASTZ Human Hg38 vs. Asiatic elephant GCF_024166365.1 # (DONE - 2022-08-22 - hiram) mkdir /hive/data/genomes/hg38/bed/lastzGCF_024166365.1.2022-08-22 cd /hive/data/genomes/hg38/bed/lastzGCF_024166365.1.2022-08-22 printf '# Asiatic elephant GCF_024166365.1 vs. Human Hg38 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Human hg38 SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Asiatic elephant 2022-07-06 GCF_024166365.1_mEleMax1_primary_haplotype SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg38/bed/lastzGCF_024166365.1.2022-08-22 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_024166365.1_mEleMax1_primary_haplotype -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 720m58.799s sed -e 's/^/ # /;' fb.hg38.chainGCF_024166365.1Link.txt # 1429926313 bases of 3272116950 (43.700%) in intersection sed -e 's/^/ # /;' fb.hg38.chainSynGCF_024166365.1Link.txt # 1358515296 bases of 3272116950 (41.518%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.chrom.sizes.txt" \ hg38 GCF_024166365.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 353m39.027s sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_024166365.1.txt # 1283436701 bases of 3272116950 (39.223%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/024/166/365/GCF_024166365.1_mEleMax1_primary_haplotype/trackData/blastz.hg38.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_024166365.1_mEleMax1_primary_haplotype /hive/data/genomes/hg38/bed/lastzGCF_024166365.1.2022-08-22/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 94m14.200s sed -e 's/^/ # /;' fb.GCF_024166365.1.chainHg38Link.txt # 1366504821 bases of 3401247148 (40.177%) in intersection sed -e 's/^/ # /;' fb.GCF_024166365.1.chainSynHg38Link.txt # 1302041922 bases of 3401247148 (38.281%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/024/166/365/GCF_024166365.1/GCF_024166365.1.chrom.sizes.txt" \ GCF_024166365.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 410m24.376s sed -e 's/^/ # /;' fb.GCF_024166365.1.chainRBest.Hg38.txt # 1284042505 bases of 3401247148 (37.752%) in intersection real 1579m17.153s user 0m0.974s sys 0m1.004s ############################################################################## # LASTZ house mouse GCA_001624675.1 vs. Mouse Mm10 # (DONE - 2023-02-06 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 printf '# Mouse Mm10 vs. house mouse GCA_001624675.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: house mouse 2016-04-26 GCA_001624675.1_NOD_ShiLtJ_v1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Mouse mm10 SEQ2_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ2_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCA_001624675.1_NOD_ShiLtJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 572m8.503s sed -e 's/^/ # /;' fb.GCA_001624675.1.chainMm10Link.txt # 2224459292 bases of 2982063250 (74.595%) in intersection sed -e 's/^/ # /;' fb.GCA_001624675.1.chainSynMm10Link.txt # 2209813247 bases of 2982063250 (74.104%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.chrom.sizes.txt" \ \ GCA_001624675.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m3.164s sed -e 's/^/ # /;' fb.GCA_001624675.1.chainRBest.Mm10.txt # 2205696172 bases of 2982063250 (73.965%) in intersection ### and for the swap cd /hive/data/genomes/mm10/bed/blastz.GCA_001624675.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCA_001624675.1_NOD_ShiLtJ_v1 /hive/data/genomes/asmHubs/allBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/trackData/lastzMm10.2023-02-06/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 107m34.257s sed -e 's/^/ # /;' fb.mm10.chainGCA_001624675.1Link.txt # 2406965836 bases of 2818974548 (85.384%) in intersection sed -e 's/^/ # /;' fb.mm10.chainSynGCA_001624675.1Link.txt # 2302191604 bases of 2818974548 (81.668%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/624/675/GCA_001624675.1/GCA_001624675.1.chrom.sizes.txt" \ \ mm10 GCA_001624675.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 86m0.955s sed -e 's/^/ # /;' fb.mm10.chainRBest.GCA_001624675.1.txt # 2200638822 bases of 2818974548 (78.065%) in intersection real 846m47.401s user 0m1.125s sys 0m1.575s ############################################################################## # LASTZ Mouse Mm10 vs. house mouse GCA_001632575.1 # (DONE - 2023-02-07 - Gerardo) mkdir /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 cd /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 printf '# house mouse GCA_001632575.1 vs. Mouse Mm10 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: house mouse 2016-05-09 GCA_001632575.1_C3H_HeJ_v1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_001632575.1_C3H_HeJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 394m43.728s sed -e 's/^/ # /;' fb.mm10.chainGCA_001632575.1Link.txt # 2458093602 bases of 2818974548 (87.198%) in intersection sed -e 's/^/ # /;' fb.mm10.chainSynGCA_001632575.1Link.txt # 2360661678 bases of 2818974548 (83.742%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt" \ mm10 GCA_001632575.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 74m28.901s sed -e 's/^/ # /;' fb.mm10.chainRBest.GCA_001632575.1.txt # 2254140497 bases of 2818974548 (79.963%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blastz.mm10.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_001632575.1_C3H_HeJ_v1 /hive/data/genomes/mm10/bed/lastzGCA_001632575.1.2023-02-07/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 110m17.627s sed -e 's/^/ # /;' fb.GCA_001632575.1.chainMm10Link.txt # 2272113623 bases of 2701131316 (84.117%) in intersection sed -e 's/^/ # /;' fb.GCA_001632575.1.chainSynMm10Link.txt # 2260408202 bases of 2701131316 (83.684%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/632/575/GCA_001632575.1/GCA_001632575.1.chrom.sizes.txt" \ GCA_001632575.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 72m53.272s sed -e 's/^/ # /;' fb.GCA_001632575.1.chainRBest.Mm10.txt # 2258449853 bases of 2701131316 (83.611%) in intersection real 652m24.059s user 0m1.118s sys 0m1.400s ############################################################################## # LASTZ Human Hg19 vs. dog GCF_014441545.1 # (DONE - 2023-02-24 - Gerardo) mkdir /hive/data/genomes/hg19/bed/lastzGCF_014441545.1.2023-02-24 cd /hive/data/genomes/hg19/bed/lastzGCF_014441545.1.2023-02-24 printf '# dog GCF_014441545.1 vs. Human Hg19 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Human hg19 SEQ1_DIR=/hive/data/genomes/hg19/hg19.2bit SEQ1_LEN=/hive/data/genomes/hg19/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: dog 2020-09-03 GCF_014441545.1_ROS_Cfam_1.0 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg19/bed/lastzGCF_014441545.1.2023-02-24 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_014441545.1_ROS_Cfam_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 737m52.454s sed -e 's/^/ # /;' fb.hg19.chainGCF_014441545.1Link.txt # 1549777055 bases of 3234851260 (47.909%) in intersection sed -e 's/^/ # /;' fb.hg19.chainSynGCF_014441545.1Link.txt # 1492573006 bases of 3234851260 (46.140%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ hg19 GCF_014441545.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 227m43.872s sed -e 's/^/ # /;' fb.hg19.chainRBest.GCF_014441545.1.txt # 1421858831 bases of 3234851260 (43.954%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/blastz.hg19.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_014441545.1_ROS_Cfam_1.0 /hive/data/genomes/hg19/bed/lastzGCF_014441545.1.2023-02-24/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 82m6.200s sed -e 's/^/ # /;' fb.GCF_014441545.1.chainHg19Link.txt # 1472641694 bases of 2396858295 (61.440%) in intersection sed -e 's/^/ # /;' fb.GCF_014441545.1.chainSynHg19Link.txt # 1434385983 bases of 2396858295 (59.844%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ GCF_014441545.1 hg19) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 236m14.653s sed -e 's/^/ # /;' fb.GCF_014441545.1.chainRBest.Hg19.txt # 1422654437 bases of 2396858295 (59.355%) in intersection real 1283m57.635s user 0m1.056s sys 0m1.272s ############################################################################## # LASTZ Human Hg19 vs. golden hamster GCF_017639785.1 # (DONE - 2023-03-01 - Gerardo) mkdir /hive/data/genomes/hg19/bed/lastzGCF_017639785.1.2023-03-01 cd /hive/data/genomes/hg19/bed/lastzGCF_017639785.1.2023-03-01 printf '# golden hamster GCF_017639785.1 vs. Human Hg19 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Human hg19 SEQ1_DIR=/hive/data/genomes/hg19/hg19.2bit SEQ1_LEN=/hive/data/genomes/hg19/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster 2021-03-30 GCF_017639785.1_BCM_Maur_2.0 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/hg19/bed/lastzGCF_017639785.1.2023-03-01 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_017639785.1_BCM_Maur_2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 288m41.670s sed -e 's/^/ # /;' fb.hg19.chainGCF_017639785.1Link.txt # 968421331 bases of 3234851260 (29.937%) in intersection sed -e 's/^/ # /;' fb.hg19.chainSynGCF_017639785.1Link.txt # 922130958 bases of 3234851260 (28.506%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt" \ hg19 GCF_017639785.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 169m40.154s sed -e 's/^/ # /;' fb.hg19.chainRBest.GCF_017639785.1.txt # 891505824 bases of 3234851260 (27.559%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/017/639/785/GCF_017639785.1_BCM_Maur_2.0/trackData/blastz.hg19.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_017639785.1_BCM_Maur_2.0 /hive/data/genomes/hg19/bed/lastzGCF_017639785.1.2023-03-01/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 54m26.973s sed -e 's/^/ # /;' fb.GCF_017639785.1.chainHg19Link.txt # 922959871 bases of 2457078271 (37.563%) in intersection sed -e 's/^/ # /;' fb.GCF_017639785.1.chainSynHg19Link.txt # 888504258 bases of 2457078271 (36.161%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt" \ GCF_017639785.1 hg19) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 176m25.926s sed -e 's/^/ # /;' fb.GCF_017639785.1.chainRBest.Hg19.txt # 893411778 bases of 2457078271 (36.361%) in intersection real 689m15.219s user 0m1.096s sys 0m1.321s ############################################################################## # LASTZ Mouse Mm10 vs. golden hamster GCF_017639785.1 # (DONE - 2023-03-01 - Gerardo) mkdir /hive/data/genomes/mm10/bed/lastzGCF_017639785.1.2023-03-01 cd /hive/data/genomes/mm10/bed/lastzGCF_017639785.1.2023-03-01 printf '# golden hamster GCF_017639785.1 vs. Mouse Mm10 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: golden hamster 2021-03-30 GCF_017639785.1_BCM_Maur_2.0 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm10/bed/lastzGCF_017639785.1.2023-03-01 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCF_017639785.1_BCM_Maur_2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 274m7.612s sed -e 's/^/ # /;' fb.mm10.chainGCF_017639785.1Link.txt # 1599131044 bases of 2818974548 (56.727%) in intersection sed -e 's/^/ # /;' fb.mm10.chainSynGCF_017639785.1Link.txt # 1494269175 bases of 2818974548 (53.008%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt" \ mm10 GCF_017639785.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 393m43.938s sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_017639785.1.txt # 1423270191 bases of 2818974548 (50.489%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/017/639/785/GCF_017639785.1_BCM_Maur_2.0/trackData/blastz.mm10.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCF_017639785.1_BCM_Maur_2.0 /hive/data/genomes/mm10/bed/lastzGCF_017639785.1.2023-03-01/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 86m14.738s sed -e 's/^/ # /;' fb.GCF_017639785.1.chainMm10Link.txt # 1516653208 bases of 2457078271 (61.726%) in intersection sed -e 's/^/ # /;' fb.GCF_017639785.1.chainSynMm10Link.txt # 1419459756 bases of 2457078271 (57.770%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt" \ GCF_017639785.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 389m15.292s sed -e 's/^/ # /;' fb.GCF_017639785.1.chainRBest.Mm10.txt # 1424688161 bases of 2457078271 (57.983%) in intersection real 1143m22.133s user 0m1.217s sys 0m1.403s ############################################################################## # LASTZ crab-eating macaque GCA_011100615.1 vs. Mouse Mm39 # (DONE - 2023-03-17 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17 cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17 printf '# Mouse Mm39 vs. crab-eating macaque GCA_011100615.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: crab-eating macaque 2020-03-10 GCA_011100615.1_Macaca_fascicularis_6.0 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Mouse mm39 SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 218m54.585s sed -e 's/^/ # /;' fb.GCA_011100615.1.chainMm39Link.txt # 912976314 bases of 2906138557 (31.415%) in intersection sed -e 's/^/ # /;' fb.GCA_011100615.1.chainSynMm39Link.txt # 869628418 bases of 2906138557 (29.924%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \ \ GCA_011100615.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 252m48.711s sed -e 's/^/ # /;' fb.GCA_011100615.1.chainRBest.Mm39.txt # 867863039 bases of 2906138557 (29.863%) in intersection ### and for the swap cd /hive/data/genomes/mm39/bed/blastz.GCA_011100615.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0 /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 62m11.211s sed -e 's/^/ # /;' fb.mm39.chainGCA_011100615.1Link.txt # 913319506 bases of 2728222451 (33.477%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCA_011100615.1Link.txt # 866991862 bases of 2728222451 (31.779%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \ \ mm39 GCA_011100615.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 398m10.453s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_011100615.1.txt # 869048496 bases of 2728222451 (31.854%) in intersection real 932m5.702s user 0m0.997s sys 0m1.331s ############################################################################## # LASTZ fission yeast GCF_000002945.1 vs. baker's yeast GCF_000146045.2 # (DONE - 2023-07-07 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/000/002/945/GCF_000002945.1_ASM294v2/trackData/lastzGCF_000146045.2.2023-07-07 cd /hive/data/genomes/asmHubs/allBuild/GCF/000/002/945/GCF_000002945.1_ASM294v2/trackData/lastzGCF_000146045.2.2023-07-07 printf '# baker's yeast GCF_000146045.2 vs. fission yeast GCF_000002945.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: fission yeast 2007-11-09 GCF_000002945.1_ASM294v2 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: baker's yeast 2014-12-17 GCF_000146045.2_R64 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/000/002/945/GCF_000002945.1_ASM294v2/trackData/lastzGCF_000146045.2.2023-07-07 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_000002945.1_ASM294v2 -qAsmId GCF_000146045.2_R64 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 6m21.750s sed -e 's/^/ # /;' fb.GCF_000002945.1.chainGCF_000146045.2Link.txt # 1782210 bases of 12591251 (14.154%) in intersection sed -e 's/^/ # /;' fb.GCF_000002945.1.chainSynGCF_000146045.2Link.txt # 25135 bases of 12591251 (0.200%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt" \ GCF_000002945.1 GCF_000146045.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 0m40.800s sed -e 's/^/ # /;' fb.GCF_000002945.1.chainRBest.GCF_000146045.2.txt # 1557514 bases of 12591251 (12.370%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCF/000/146/045/GCF_000146045.2_R64/trackData/blastz.GCF_000002945.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_000002945.1_ASM294v2 -qAsmId GCF_000146045.2_R64 /hive/data/genomes/asmHubs/allBuild/GCF/000/002/945/GCF_000002945.1_ASM294v2/trackData/lastzGCF_000146045.2.2023-07-07/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 1m10.192s sed -e 's/^/ # /;' fb.GCF_000146045.2.chainGCF_000002945.1Link.txt # 1916992 bases of 12157105 (15.768%) in intersection sed -e 's/^/ # /;' fb.GCF_000146045.2.chainSynGCF_000002945.1Link.txt # 11694 bases of 12157105 (0.096%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt" \ GCF_000146045.2 GCF_000002945.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 0m37.702s sed -e 's/^/ # /;' fb.GCF_000146045.2.chainRBest.GCF_000002945.1.txt # 1571707 bases of 12157105 (12.928%) in intersection real 8m57.345s user 0m2.512s sys 0m3.487s ############################################################################## # LASTZ sheep GCF_016772045.2 vs. Sheep OviAri3 # (DONE - 2024-03-23 - Gerardo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23 cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23 printf '# Sheep OviAri3 vs. sheep GCF_016772045.2 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: Sheep oviAri3 SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.2bit SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 429m12.994s sed -e 's/^/ # /;' fb.GCF_016772045.2.chainOviAri3Link.txt # 2525078490 bases of 2654063983 (95.140%) in intersection sed -e 's/^/ # /;' fb.GCF_016772045.2.chainSynOviAri3Link.txt # 2482973739 bases of 2654063983 (93.554%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ \ GCF_016772045.2 oviAri3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 85m16.406s sed -e 's/^/ # /;' fb.GCF_016772045.2.chainRBest.OviAri3.txt # 2466724548 bases of 2654063983 (92.941%) in intersection ### and for the swap cd /hive/data/genomes/oviAri3/bed/blastz.GCF_016772045.2.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 214m0.944s sed -e 's/^/ # /;' fb.oviAri3.chainGCF_016772045.2Link.txt # 2499925356 bases of 2619054388 (95.451%) in intersection sed -e 's/^/ # /;' fb.oviAri3.chainSynGCF_016772045.2Link.txt # 2475557584 bases of 2619054388 (94.521%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ \ oviAri3 GCF_016772045.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 84m46.671s sed -e 's/^/ # /;' fb.oviAri3.chainRBest.GCF_016772045.2.txt # 2470476691 bases of 2619054388 (94.327%) in intersection real 813m22.700s user 0m3.066s sys 0m3.274s ############################################################################## + +# LASTZ Sheep OviAri4 vs. goat GCF_001704415.2 +# (DONE - 2024-06-07 - lrnassar) + + mkdir /hive/data/genomes/oviAri4/bed/lastzGCF_001704415.2.2024-06-07 + cd /hive/data/genomes/oviAri4/bed/lastzGCF_001704415.2.2024-06-07 + + printf '# goat GCF_001704415.2 vs. Sheep OviAri4 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Sheep oviAri4 +SEQ1_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit +SEQ1_LEN=/hive/data/genomes/oviAri4/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/oviAri4/bed/lastzGCF_001704415.2.2024-06-07 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_001704415.2_ARS1.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1322m31.500s + + sed -e 's/^/ # /;' fb.oviAri4.chainGCF_001704415.2Link.txt + # 2522278589 bases of 2615516299 (96.435%) in intersection + sed -e 's/^/ # /;' fb.oviAri4.chainSynGCF_001704415.2Link.txt + # 2482402802 bases of 2615516299 (94.911%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + oviAri4 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 199m30.609s + + sed -e 's/^/ # /;' fb.oviAri4.chainRBest.GCF_001704415.2.txt + # 2477685011 bases of 2615516299 (94.730%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.oviAri4.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/oviAri4/bed/lastzGCF_001704415.2.2024-06-07/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 1031m1.896s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainOviAri4Link.txt + # 2564341511 bases of 2922617086 (87.741%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynOviAri4Link.txt + # 2514390106 bases of 2922617086 (86.032%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + GCF_001704415.2 oviAri4) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 180m47.478s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.OviAri4.txt + # 2474132806 bases of 2922617086 (84.655%) in intersection + +############################################################################## +### elapsed time: 45h 34m 01s + +Sun Jun 9 08:32:19 PDT 2024 +################################################################## + +