9d4bef0d3eb7ba60d763868e2db43256281e38ab hiram Fri Oct 22 13:31:37 2021 -0700 lastz runs to golden hamster refs #28333 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 85106ac..e37d669 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1,347 +1,852 @@ ############################################################################## # 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 +##############################################################################