1ac19241d8c26d55fe304ed17a3cc41d2c3c5115 jnavarr5 Thu Sep 5 15:20:13 2024 -0700 Adding makedocs for liftOver files created, refs #34305 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index 9a2659d..ceae701 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -14361,15 +14361,418 @@ \ -target2bit="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/023/856/395/GCA_023856395.1/GCA_023856395.1.chrom.sizes.txt" \ GCA_023856395.1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 224m13.370s sed -e 's/^/ # /;' fb.GCA_023856395.1.chainRBest.Hg38.txt # 858590864 bases of 2119204330 (40.515%) in intersection real 854m18.020s user 0m2.527s sys 0m2.820s ############################################################################## +# LASTZ Human Hg38 vs. domestic yak GCA_005887515.3 +# (DONE - 2024-09-03 - jairo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03 + cd /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03 + + printf '# domestic yak GCA_005887515.3 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: domestic yak 2019-06-10 GCA_005887515.3_BosGru3.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_005887515.3_BosGru3.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 518m35.100s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_005887515.3Link.txt + # 1392640940 bases of 3299210039 (42.211%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_005887515.3Link.txt + # 1324979599 bases of 3299210039 (40.161%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + hg38 GCA_005887515.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 305m47.663s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_005887515.3.txt + # 1246857312 bases of 3299210039 (37.793%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_005887515.3_BosGru3.1 /hive/data/genomes/hg38/bed/lastzGCA_005887515.3.2024-09-03/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 81m25.155s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainHg38Link.txt + # 1394265201 bases of 2831460571 (49.242%) in intersection + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainSynHg38Link.txt + # 1347828299 bases of 2831460571 (47.602%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + GCA_005887515.3 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 861m27.454s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainRBest.Hg38.txt + # 1250496047 bases of 2831460571 (44.164%) in intersection + +############################################################################## +# LASTZ Human Hg38 vs. sugar glider GCA_028583685.1 +# (DONE - 2024-09-03 - jairo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03 + cd /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03 + + printf '# sugar glider GCA_028583685.1 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: sugar glider 2023-02-10 GCA_028583685.1_PetGlider_PUasm1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_028583685.1_PetGlider_PUasm1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 329m31.325s + + sed -e 's/^/ # /;' fb.hg38.chainGCA_028583685.1Link.txt + # 254830797 bases of 3299210039 (7.724%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCA_028583685.1Link.txt + # 109229739 bases of 3299210039 (3.311%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt" \ + hg38 GCA_028583685.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 442m16.187s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCA_028583685.1.txt + # 214015545 bases of 3299210039 (6.487%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/028/583/685/GCA_028583685.1_PetGlider_PUasm1.0/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_028583685.1_PetGlider_PUasm1.0 /hive/data/genomes/hg38/bed/lastzGCA_028583685.1.2024-09-03/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 24m48.018s + + sed -e 's/^/ # /;' fb.GCA_028583685.1.chainHg38Link.txt + # 247775279 bases of 3464704272 (7.151%) in intersection + sed -e 's/^/ # /;' fb.GCA_028583685.1.chainSynHg38Link.txt + # 106375970 bases of 3464704272 (3.070%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/028/583/685/GCA_028583685.1/GCA_028583685.1.chrom.sizes.txt" \ + GCA_028583685.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 453m13.738s + + sed -e 's/^/ # /;' fb.GCA_028583685.1.chainRBest.Hg38.txt + # 213968297 bases of 3464704272 (6.176%) in intersection + +############################################################################## +############################################################################## +# LASTZ Human Hg38 vs. red deer GCF_910594005.1 +# (DONE - 2024-08-29 - jairo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29 + cd /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29 + + printf '# red deer GCF_910594005.1 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: red deer 2021-07-07 GCF_910594005.1_mCerEla1.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_910594005.1_mCerEla1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1617m14.834s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_910594005.1Link.txt + # 1462456359 bases of 3299210039 (44.327%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_910594005.1Link.txt + # 1392968298 bases of 3299210039 (42.221%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt" \ + hg38 GCF_910594005.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 257m51.239s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_910594005.1.txt + # 1307680530 bases of 3299210039 (39.636%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/910/594/005/GCF_910594005.1_mCerEla1.1/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_910594005.1_mCerEla1.1 /hive/data/genomes/hg38/bed/lastzGCF_910594005.1.2024-08-29/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 99m46.211s + + sed -e 's/^/ # /;' fb.GCF_910594005.1.chainHg38Link.txt + # 1388751208 bases of 2886603524 (48.110%) in intersection + sed -e 's/^/ # /;' fb.GCF_910594005.1.chainSynHg38Link.txt + # 1329736375 bases of 2886603524 (46.066%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/910/594/005/GCF_910594005.1/GCF_910594005.1.chrom.sizes.txt" \ + GCF_910594005.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 274m8.274s + + sed -e 's/^/ # /;' fb.GCF_910594005.1.chainRBest.Hg38.txt + # 1308109027 bases of 2886603524 (45.317%) in intersection + +############################################################################## +############################################################################## +# LASTZ Human Hg38 vs. sheep GCF_016772045.2 +# (DONE - 2024-08-29 - jairo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29 + cd /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29 + + printf '# sheep GCF_016772045.2 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: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId 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 765m43.186s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_016772045.2Link.txt + # 1427686356 bases of 3299210039 (43.274%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_016772045.2Link.txt + # 1363288307 bases of 3299210039 (41.322%) 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" \ + hg38 GCF_016772045.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 282m27.955s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_016772045.2.txt + # 1280579203 bases of 3299210039 (38.815%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 /hive/data/genomes/hg38/bed/lastzGCF_016772045.2.2024-08-29/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 75m52.789s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainHg38Link.txt + # 1329798265 bases of 2654063983 (50.104%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainSynHg38Link.txt + # 1287911784 bases of 2654063983 (48.526%) 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 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 281m46.146s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainRBest.Hg38.txt + # 1281122070 bases of 2654063983 (48.270%) in intersection + +############################################################################## +############################################################################## +# LASTZ Human Hg38 vs. Bactrian camel GCF_000767855.1 +# (DONE - 2024-08-29 - jairo) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29 + cd /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29 + + printf '# Bactrian camel GCF_000767855.1 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: Bactrian camel 2014-10-23 GCF_000767855.1_Ca_bactrianus_MBC_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_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 759m53.919s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_000767855.1Link.txt + # 1536856108 bases of 3299210039 (46.583%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_000767855.1Link.txt + # 1468539068 bases of 3299210039 (44.512%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \ + hg38 GCF_000767855.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 182m17.263s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_000767855.1.txt + # 1372910494 bases of 3299210039 (41.613%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/767/855/GCF_000767855.1_Ca_bactrianus_MBC_1.0/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_1.0 /hive/data/genomes/hg38/bed/lastzGCF_000767855.1.2024-08-29/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 81m24.949s + + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainHg38Link.txt + # 1409283773 bases of 1992663268 (70.724%) in intersection + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainSynHg38Link.txt + # 1372565487 bases of 1992663268 (68.881%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \ + GCF_000767855.1 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 166m30.684s + + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainRBest.Hg38.txt + # 1373576819 bases of 1992663268 (68.932%) in intersection + +##############################################################################