b85993b9ee03fc6b36fc752de2051f2eb06f7e83 gperez2 Sat Aug 12 13:36:04 2023 -0700 dm6 vs. GCF_016746395.2/GCF_004382195.2/GCF_018902025.1/GCF_009870125.1/GCF_017639315.1/GCF_016746365.2, lastz/chain/net run for user, refs #31548 diff --git src/hg/makeDb/doc/dm6/lastzRuns.txt src/hg/makeDb/doc/dm6/lastzRuns.txt index 962f7fc..b927c24 100644 --- src/hg/makeDb/doc/dm6/lastzRuns.txt +++ src/hg/makeDb/doc/dm6/lastzRuns.txt @@ -1,180 +1,678 @@ ############################################################################## # LASTZ D. melanogaster Dm6 vs. D. pseudoobscura Dp3 (DONE - 2022-04-22 - 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 \ dm6 dp3 other other) \ > dm6.dp3_20220422.log 2>&1 & # check the total time grep -w real dm6.dp3_20220422.log | tail -1 | sed -e 's/^/ # /;' # real 35m30.881s ############################################################################## # LASTZ D. melanogaster Dm6 vs. D. pseudoobscura Dp3 # (DONE - 2022-04-22 - Gerardo) mkdir /hive/data/genomes/dm6/bed/lastzDp3.2022-04-22 cd /hive/data/genomes/dm6/bed/lastzDp3.2022-04-22 printf '# D. pseudoobscura Dp3 vs. D. melanogaster Dm6 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: D. melanogaster dm6 SEQ1_DIR=/hive/data/genomes/dm6/dm6.2bit SEQ1_LEN=/hive/data/genomes/dm6/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: D. pseudoobscura dp3 SEQ2_DIR=/hive/data/genomes/dp3/dp3.2bit SEQ2_LEN=/hive/data/genomes/dp3/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/dm6/bed/lastzDp3.2022-04-22 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 17m17.531s sed -e 's/^/ # /;' fb.dm6.chainDp3Link.txt # 76846431 bases of 142573024 (53.900%) in intersection sed -e 's/^/ # /;' fb.dm6.chainSynDp3Link.txt # 68520128 bases of 142573024 (48.060%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ dm6 dp3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 6m6.187s sed -e 's/^/ # /;' fb.dm6.chainRBest.Dp3.txt # 74465237 bases of 142573024 (52.230%) in intersection ### and for the swap cd /hive/data/genomes/dp3/bed/blastz.dm6.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ /hive/data/genomes/dm6/bed/lastzDp3.2022-04-22/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 4m56.014s sed -e 's/^/ # /;' fb.dp3.chainDm6Link.txt # 77597252 bases of 134584124 (57.657%) in intersection sed -e 's/^/ # /;' fb.dp3.chainSynDm6Link.txt # 71073398 bases of 134584124 (52.810%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ dp3 dm6) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 7m10.767s sed -e 's/^/ # /;' fb.dp3.chainRBest.Dm6.txt # 74511442 bases of 134584124 (55.364%) in intersection real 35m30.881s user 0m1.225s sys 0m0.802s ############################################################################## ############################################################################## # LASTZ Zebrafish DanRer11 vs. D. melanogaster Dm6 # (DONE - 2022-09-13 - hiram) # per user request redmine #29981 mkdir /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13 cd /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13 printf '# D. melanogaster Dm6 vs. Zebrafish DanRer11 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Zebrafish danRer11 SEQ1_DIR=/hive/data/genomes/danRer11/danRer11.2bit SEQ1_LEN=/hive/data/genomes/danRer11/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: D. melanogaster dm6 SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 13m28.637s sed -e 's/^/ # /;' fb.danRer11.chainDm6Link.txt # 9922943 bases of 1674677181 (0.593%) in intersection sed -e 's/^/ # /;' fb.danRer11.chainSynDm6Link.txt # 65331 bases of 1674677181 (0.004%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ danRer11 dm6) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 11m31.879s sed -e 's/^/ # /;' fb.danRer11.chainRBest.Dm6.txt # 3483314 bases of 1674677181 (0.208%) in intersection ### and for the swap cd /hive/data/genomes/dm6/bed/blastz.danRer11.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ /hive/data/genomes/danRer11/bed/lastzDm6.2022-09-13/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 1m12.711s sed -e 's/^/ # /;' fb.dm6.chainDanRer11Link.txt # 4086744 bases of 142573024 (2.866%) in intersection sed -e 's/^/ # /;' fb.dm6.chainSynDanRer11Link.txt # 42241 bases of 142573024 (0.030%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ \ \ dm6 danRer11) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 8m35.092s sed -e 's/^/ # /;' fb.dm6.chainRBest.DanRer11.txt # 3396581 bases of 142573024 (2.382%) in intersection real 34m48.592s user 0m0.866s sys 0m0.812s ############################################################################## +# LASTZ D. melanogaster Dm6 vs. flies GCF_016746395.2 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/dm6/bed/lastzGCF_016746395.2.2023-06-28 + cd /hive/data/genomes/dm6/bed/lastzGCF_016746395.2.2023-06-28 + + printf '# flies GCF_016746395.2 vs. D. melanogaster Dm6 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: D. melanogaster dm6 +SEQ1_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ1_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: flies 2021-10-05 GCF_016746395.2_Prin_Dsim_3.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/dm6/bed/lastzGCF_016746395.2.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_016746395.2_Prin_Dsim_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 16m29.048s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_016746395.2Link.txt + # 116628498 bases of 143726002 (81.146%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_016746395.2Link.txt + # 109133106 bases of 143726002 (75.931%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.chrom.sizes.txt" \ + dm6 GCF_016746395.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 6m57.512s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_016746395.2.txt + # 110914317 bases of 143726002 (77.171%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/746/395/GCF_016746395.2_Prin_Dsim_3.1/trackData/blastz.dm6.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_016746395.2_Prin_Dsim_3.1 /hive/data/genomes/dm6/bed/lastzGCF_016746395.2.2023-06-28/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 6m45.642s + + sed -e 's/^/ # /;' fb.GCF_016746395.2.chainDm6Link.txt + # 115117913 bases of 131663590 (87.433%) in intersection + sed -e 's/^/ # /;' fb.GCF_016746395.2.chainSynDm6Link.txt + # 108978459 bases of 131663590 (82.770%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/746/395/GCF_016746395.2/GCF_016746395.2.chrom.sizes.txt" \ + GCF_016746395.2 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 6m37.033s + + sed -e 's/^/ # /;' fb.GCF_016746395.2.chainRBest.Dm6.txt + # 110819698 bases of 131663590 (84.169%) in intersection + +real 36m52.324s +user 0m2.130s +sys 0m2.350s +############################################################################## +# LASTZ flies GCF_004382195.2 vs. D. melanogaster Dm6 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/004/382/195/GCF_004382195.2_ASM438219v2/trackData/lastzDm6.2023-06-28 + cd /hive/data/genomes/asmHubs/allBuild/GCF/004/382/195/GCF_004382195.2_ASM438219v2/trackData/lastzDm6.2023-06-28 + + printf '# D. melanogaster Dm6 vs. flies GCF_004382195.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: flies 2019-04-16 GCF_004382195.2_ASM438219v2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: D. melanogaster dm6 +SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/004/382/195/GCF_004382195.2_ASM438219v2/trackData/lastzDm6.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_004382195.2_ASM438219v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 19m16.264s + + sed -e 's/^/ # /;' fb.GCF_004382195.2.chainDm6Link.txt + # 121693100 bases of 153084571 (79.494%) in intersection + sed -e 's/^/ # /;' fb.GCF_004382195.2.chainSynDm6Link.txt + # 110266303 bases of 153084571 (72.030%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.chrom.sizes.txt" \ + \ + GCF_004382195.2 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 7m9.512s + + sed -e 's/^/ # /;' fb.GCF_004382195.2.chainRBest.Dm6.txt + # 111536509 bases of 153084571 (72.859%) in intersection + + ### and for the swap + + cd /hive/data/genomes/dm6/bed/blastz.GCF_004382195.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_004382195.2_ASM438219v2 /hive/data/genomes/asmHubs/allBuild/GCF/004/382/195/GCF_004382195.2_ASM438219v2/trackData/lastzDm6.2023-06-28/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 5m59.898s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_004382195.2Link.txt + # 116610658 bases of 143726002 (81.134%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_004382195.2Link.txt + # 108724924 bases of 143726002 (75.647%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/004/382/195/GCF_004382195.2/GCF_004382195.2.chrom.sizes.txt" \ + \ + dm6 GCF_004382195.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 6m40.942s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_004382195.2.txt + # 111367549 bases of 143726002 (77.486%) in intersection + +real 39m10.546s +user 0m2.242s +sys 0m2.425s +############################################################################## +# LASTZ flies GCF_018902025.1 vs. D. melanogaster Dm6 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/018/902/025/GCF_018902025.1_UCI_dwil_1.1/trackData/lastzDm6.2023-06-28 + cd /hive/data/genomes/asmHubs/allBuild/GCF/018/902/025/GCF_018902025.1_UCI_dwil_1.1/trackData/lastzDm6.2023-06-28 + + printf '# D. melanogaster Dm6 vs. flies GCF_018902025.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: flies 2021-06-16 GCF_018902025.1_UCI_dwil_1.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: D. melanogaster dm6 +SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/018/902/025/GCF_018902025.1_UCI_dwil_1.1/trackData/lastzDm6.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_018902025.1_UCI_dwil_1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 14m57.691s + + sed -e 's/^/ # /;' fb.GCF_018902025.1.chainDm6Link.txt + # 68885615 bases of 246985538 (27.891%) in intersection + sed -e 's/^/ # /;' fb.GCF_018902025.1.chainSynDm6Link.txt + # 49233910 bases of 246985538 (19.934%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.chrom.sizes.txt" \ + \ + GCF_018902025.1 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 7m42.837s + + sed -e 's/^/ # /;' fb.GCF_018902025.1.chainRBest.Dm6.txt + # 54712421 bases of 246985538 (22.152%) in intersection + + ### and for the swap + + cd /hive/data/genomes/dm6/bed/blastz.GCF_018902025.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_018902025.1_UCI_dwil_1.1 /hive/data/genomes/asmHubs/allBuild/GCF/018/902/025/GCF_018902025.1_UCI_dwil_1.1/trackData/lastzDm6.2023-06-28/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 4m7.474s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_018902025.1Link.txt + # 56380331 bases of 143726002 (39.228%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_018902025.1Link.txt + # 47257734 bases of 143726002 (32.880%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/018/902/025/GCF_018902025.1/GCF_018902025.1.chrom.sizes.txt" \ + \ + dm6 GCF_018902025.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 6m26.288s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_018902025.1.txt + # 54650787 bases of 143726002 (38.024%) in intersection + +real 33m17.691s +user 0m2.185s +sys 0m2.432s +############################################################################## +# LASTZ flies GCF_009870125.1 vs. D. melanogaster Dm6 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/009/870/125/GCF_009870125.1_UCI_Dpse_MV25/trackData/lastzDm6.2023-06-28 + cd /hive/data/genomes/asmHubs/allBuild/GCF/009/870/125/GCF_009870125.1_UCI_Dpse_MV25/trackData/lastzDm6.2023-06-28 + + printf '# D. melanogaster Dm6 vs. flies GCF_009870125.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: flies 2020-03-03 GCF_009870125.1_UCI_Dpse_MV25 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: D. melanogaster dm6 +SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/009/870/125/GCF_009870125.1_UCI_Dpse_MV25/trackData/lastzDm6.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_009870125.1_UCI_Dpse_MV25 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 16m58.357s + + sed -e 's/^/ # /;' fb.GCF_009870125.1.chainDm6Link.txt + # 81798982 bases of 163282969 (50.096%) in intersection + sed -e 's/^/ # /;' fb.GCF_009870125.1.chainSynDm6Link.txt + # 71888836 bases of 163282969 (44.027%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.chrom.sizes.txt" \ + \ + GCF_009870125.1 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 8m36.457s + + sed -e 's/^/ # /;' fb.GCF_009870125.1.chainRBest.Dm6.txt + # 76318824 bases of 163282969 (46.740%) in intersection + + ### and for the swap + + cd /hive/data/genomes/dm6/bed/blastz.GCF_009870125.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_009870125.1_UCI_Dpse_MV25 /hive/data/genomes/asmHubs/allBuild/GCF/009/870/125/GCF_009870125.1_UCI_Dpse_MV25/trackData/lastzDm6.2023-06-28/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 5m7.710s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_009870125.1Link.txt + # 78661483 bases of 143726002 (54.730%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_009870125.1Link.txt + # 71517531 bases of 143726002 (49.760%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/009/870/125/GCF_009870125.1/GCF_009870125.1.chrom.sizes.txt" \ + \ + dm6 GCF_009870125.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 6m42.864s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_009870125.1.txt + # 76320323 bases of 143726002 (53.101%) in intersection + +real 37m28.485s +user 0m2.190s +sys 0m2.336s +############################################################################## +# LASTZ flies GCF_017639315.1 vs. D. melanogaster Dm6 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/017/639/315/GCF_017639315.1_ASM1763931v2/trackData/lastzDm6.2023-06-28 + cd /hive/data/genomes/asmHubs/allBuild/GCF/017/639/315/GCF_017639315.1_ASM1763931v2/trackData/lastzDm6.2023-06-28 + + printf '# D. melanogaster Dm6 vs. flies GCF_017639315.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: flies 2021-07-16 GCF_017639315.1_ASM1763931v2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: D. melanogaster dm6 +SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/017/639/315/GCF_017639315.1_ASM1763931v2/trackData/lastzDm6.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_017639315.1_ASM1763931v2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 25m57.774s + + sed -e 's/^/ # /;' fb.GCF_017639315.1.chainDm6Link.txt + # 88495851 bases of 213817545 (41.388%) in intersection + sed -e 's/^/ # /;' fb.GCF_017639315.1.chainSynDm6Link.txt + # 81059485 bases of 213817545 (37.911%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.chrom.sizes.txt" \ + \ + GCF_017639315.1 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 5m41.052s + + sed -e 's/^/ # /;' fb.GCF_017639315.1.chainRBest.Dm6.txt + # 84169214 bases of 213817545 (39.365%) in intersection + + ### and for the swap + + cd /hive/data/genomes/dm6/bed/blastz.GCF_017639315.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_017639315.1_ASM1763931v2 /hive/data/genomes/asmHubs/allBuild/GCF/017/639/315/GCF_017639315.1_ASM1763931v2/trackData/lastzDm6.2023-06-28/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 5m37.212s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_017639315.1Link.txt + # 86322512 bases of 143726002 (60.060%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_017639315.1Link.txt + # 80373263 bases of 143726002 (55.921%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/017/639/315/GCF_017639315.1/GCF_017639315.1.chrom.sizes.txt" \ + \ + dm6 GCF_017639315.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 5m8.955s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_017639315.1.txt + # 84064054 bases of 143726002 (58.489%) in intersection + +real 42m28.493s +user 0m2.250s +sys 0m2.471s +############################################################################## +# LASTZ flies GCF_016746365.2 vs. D. melanogaster Dm6 +# (DONE - 2023-06-28 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/746/365/GCF_016746365.2_Prin_Dyak_Tai18E2_2.1/trackData/lastzDm6.2023-06-28 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/746/365/GCF_016746365.2_Prin_Dyak_Tai18E2_2.1/trackData/lastzDm6.2023-06-28 + + printf '# D. melanogaster Dm6 vs. flies GCF_016746365.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: flies 2021-07-30 GCF_016746365.2_Prin_Dyak_Tai18E2_2.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: D. melanogaster dm6 +SEQ2_DIR=/hive/data/genomes/dm6/dm6.2bit +SEQ2_LEN=/hive/data/genomes/dm6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/746/365/GCF_016746365.2_Prin_Dyak_Tai18E2_2.1/trackData/lastzDm6.2023-06-28 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016746365.2_Prin_Dyak_Tai18E2_2.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 22m44.980s + + sed -e 's/^/ # /;' fb.GCF_016746365.2.chainDm6Link.txt + # 117036776 bases of 147899117 (79.133%) in intersection + sed -e 's/^/ # /;' fb.GCF_016746365.2.chainSynDm6Link.txt + # 105358746 bases of 147899117 (71.237%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.chrom.sizes.txt" \ + \ + GCF_016746365.2 dm6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 8m40.879s + + sed -e 's/^/ # /;' fb.GCF_016746365.2.chainRBest.Dm6.txt + # 107314533 bases of 147899117 (72.559%) in intersection + + ### and for the swap + + cd /hive/data/genomes/dm6/bed/blastz.GCF_016746365.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016746365.2_Prin_Dyak_Tai18E2_2.1 /hive/data/genomes/asmHubs/allBuild/GCF/016/746/365/GCF_016746365.2_Prin_Dyak_Tai18E2_2.1/trackData/lastzDm6.2023-06-28/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 6m21.968s + + sed -e 's/^/ # /;' fb.dm6.chainGCF_016746365.2Link.txt + # 111904472 bases of 143726002 (77.860%) in intersection + sed -e 's/^/ # /;' fb.dm6.chainSynGCF_016746365.2Link.txt + # 103903783 bases of 143726002 (72.293%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/746/365/GCF_016746365.2/GCF_016746365.2.chrom.sizes.txt" \ + \ + dm6 GCF_016746365.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 7m11.316s + + sed -e 's/^/ # /;' fb.dm6.chainRBest.GCF_016746365.2.txt + # 107383728 bases of 143726002 (74.714%) in intersection + +real 45m2.386s +user 0m2.208s +sys 0m2.449s +##############################################################################