7d0bd2b7d089f94c9a8260c417246d4dbfce2523 mspeir Sat Mar 29 18:51:22 2025 -0700 adding make docs for several lastz runs from the last 6 months or so diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index e97b4148764..ef048be1651 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -2618,30 +2618,87 @@ -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 water buffalo GCF_019923935.1 vs. Cow BosTau9 +# (DONE - 2024-01-05 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 + + printf '# Cow BosTau9 vs. water buffalo GCF_019923935.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzBosTau9.2024-01-05 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 2623m44.119s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainBosTau9Link.txt + # 2522886084 bases of 2622460639 (96.203%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynBosTau9Link.txt + # 2484746893 bases of 2622460639 (94.749%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ + \ + GCF_019923935.1 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 146m41.533s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.BosTau9.txt + # 2476483890 bases of 2622460639 (94.434%) in intersection + +real 4287m53.907s +user 0m2.895s +sys 0m2.314s + ############################################################################## # 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 @@ -2871,30 +2928,238 @@ -query2bit="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.chrom.sizes.txt" \ GCA_963855885.1 GCA_963853865.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 20m44.501s sed -e 's/^/ # /;' fb.GCA_963855885.1.chainRBest.GCA_963853865.1.txt # 42397910 bases of 457736400 (9.263%) in intersection real 75m47.883s user 0m2.731s sys 0m3.078s + +############################################################################## +# LASTZ white-tufted-ear marmoset GCA_011100555.2 vs. tamarin GCA_004024885.1 +# (DONE - 2024-08-01 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_004024885.1.2024-08-01 + cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_004024885.1.2024-08-01 + + printf '# tamarin GCA_004024885.1 vs. white-tufted-ear marmoset GCA_011100555.2 +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: white-tufted-ear marmoset 2021-04-28 GCA_011100555.2_mCalJa1.2.pat.X +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: tamarin 2019-01-15 GCA_004024885.1_SagImp_v1_BIUU +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/004/024/885/GCA_004024885.1/GCA_004024885.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/004/024/885/GCA_004024885.1/GCA_004024885.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_004024885.1.2024-08-01 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_011100555.2_mCalJa1.2.pat.X -qAsmId GCA_004024885.1_SagImp_v1_BIUU -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1920m6.340s + + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainGCA_004024885.1Link.txt + # 2622898633 bases of 2874881015 (91.235%) in intersection + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainSynGCA_004024885.1Link.txt + # 2461674238 bases of 2874881015 (85.627%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/004/024/885/GCA_004024885.1/GCA_004024885.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/004/024/885/GCA_004024885.1/GCA_004024885.1.chrom.sizes.txt" \ + GCA_011100555.2 GCA_004024885.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 325m6.489s + + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainRBest.GCA_004024885.1.txt + # 2437380180 bases of 2874881015 (84.782%) in intersection + +real 8390m32.612s +user 0m10.684s +sys 0m7.895s + +############################################################################## +# LASTZ cotton-top tamarin GCA_031835075.1 vs. white-tufted-ear marmoset GCA_011100555.2 +# (DONE - 2024-08-01 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/031/835/075/GCA_031835075.1_ASM3183507v1/trackData/lastzGCA_011100555.2.2024-08-01 + cd /hive/data/genomes/asmHubs/allBuild/GCA/031/835/075/GCA_031835075.1_ASM3183507v1/trackData/lastzGCA_011100555.2.2024-08-01 + + printf '# white-tufted-ear marmoset GCA_011100555.2 vs. cotton-top tamarin GCA_031835075.1 +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: cotton-top tamarin 2023-09-25 GCA_031835075.1_ASM3183507v1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/031/835/075/GCA_031835075.1/GCA_031835075.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/031/835/075/GCA_031835075.1/GCA_031835075.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: white-tufted-ear marmoset 2021-04-28 GCA_011100555.2_mCalJa1.2.pat.X +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/031/835/075/GCA_031835075.1_ASM3183507v1/trackData/lastzGCA_011100555.2.2024-08-01 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_031835075.1_ASM3183507v1 -qAsmId GCA_011100555.2_mCalJa1.2.pat.X -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1708m35.770s + + sed -e 's/^/ # /;' fb.GCA_031835075.1.chainGCA_011100555.2Link.txt + # 2925735211 bases of 3240197989 (90.295%) in intersection + sed -e 's/^/ # /;' fb.GCA_031835075.1.chainSynGCA_011100555.2Link.txt + # 2597957271 bases of 3240197989 (80.179%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/031/835/075/GCA_031835075.1/GCA_031835075.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/031/835/075/GCA_031835075.1/GCA_031835075.1.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt" \ + GCA_031835075.1 GCA_011100555.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 207m21.175s + + sed -e 's/^/ # /;' fb.GCA_031835075.1.chainRBest.GCA_011100555.2.txt + # 2495702036 bases of 3240197989 (77.023%) in intersection + +real 3815m47.304s +user 0m5.699s +sys 0m5.441s + +############################################################################## +# LASTZ white-tufted-ear marmoset GCA_011100555.2 vs. golden lion tamarin GCA_028533165.1 +# (DONE - 2024-08-08 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_028533165.1.2024-08-08 + cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_028533165.1.2024-08-08 + + printf '# golden lion tamarin GCA_028533165.1 vs. white-tufted-ear marmoset GCA_011100555.2 +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: white-tufted-ear marmoset 2021-04-28 GCA_011100555.2_mCalJa1.2.pat.X +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: golden lion tamarin 2023-02-09 GCA_028533165.1_Leontopithecus_rosalia_HiC +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/028/533/165/GCA_028533165.1/GCA_028533165.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/028/533/165/GCA_028533165.1/GCA_028533165.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/011/100/555/GCA_011100555.2_mCalJa1.2.pat.X/trackData/lastzGCA_028533165.1.2024-08-08 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_011100555.2_mCalJa1.2.pat.X -qAsmId GCA_028533165.1_Leontopithecus_rosalia_HiC -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 881m54.590s + + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainGCA_028533165.1Link.txt + # 2618676644 bases of 2874881015 (91.088%) in intersection + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainSynGCA_028533165.1Link.txt + # 2388168606 bases of 2874881015 (83.070%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/555/GCA_011100555.2/GCA_011100555.2.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/028/533/165/GCA_028533165.1/GCA_028533165.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/028/533/165/GCA_028533165.1/GCA_028533165.1.chrom.sizes.txt" \ + GCA_011100555.2 GCA_028533165.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 216m28.727s + + sed -e 's/^/ # /;' fb.GCA_011100555.2.chainRBest.GCA_028533165.1.txt + # 2454193558 bases of 2874881015 (85.367%) in intersection + +real 2216m31.451s +user 0m11.874s +sys 0m10.111s + ############################################################################## # LASTZ domestic cattle GCF_002263795.3 vs. Bactrian camel GCF_000767855.1 # (DONE - 2024-08-29 - jairo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 printf '# Bactrian camel GCF_000767855.1 vs. domestic cattle GCF_002263795.3 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 @@ -3277,15 +3542,100 @@ # 2663500489 bases of 2724980740 (97.744%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.chrom.sizes.txt" \ GCA_000003205.6 GCF_002263795.3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 115m10.092s sed -e 's/^/ # /;' fb.GCA_000003205.6.chainRBest.GCF_002263795.3.txt # 2640372564 bases of 2724980740 (96.895%) in intersection ############################################################################## + +# LASTZ Norway rat GCF_036323735.1 vs. Mouse Mm10 +# (DONE - 2025-02-26 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/036/323/735/GCF_036323735.1_GRCr8/trackData/lastzMm10.2025-02-26 + cd /hive/data/genomes/asmHubs/allBuild/GCF/036/323/735/GCF_036323735.1_GRCr8/trackData/lastzMm10.2025-02-26 + + printf '# Mouse Mm10 vs. Norway rat GCF_036323735.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Norway rat 2024-01-31 GCF_036323735.1_GRCr8 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.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/GCF/036/323/735/GCF_036323735.1_GRCr8/trackData/lastzMm10.2025-02-26 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_036323735.1_GRCr8 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1670m29.656s + + sed -e 's/^/ # /;' fb.GCF_036323735.1.chainMm10Link.txt + # 1976586833 bases of 2849581192 (69.364%) in intersection + sed -e 's/^/ # /;' fb.GCF_036323735.1.chainSynMm10Link.txt + # 1793765353 bases of 2849581192 (62.948%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.chrom.sizes.txt" \ + \ + GCF_036323735.1 mm10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 464m54.479s + + sed -e 's/^/ # /;' fb.GCF_036323735.1.chainRBest.Mm10.txt + # 1763029185 bases of 2849581192 (61.870%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm10/bed/blastz.GCF_036323735.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_036323735.1_GRCr8 /hive/data/genomes/asmHubs/allBuild/GCF/036/323/735/GCF_036323735.1_GRCr8/trackData/lastzMm10.2025-02-26/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 290m5.196s + + sed -e 's/^/ # /;' fb.mm10.chainGCF_036323735.1Link.txt + # 1970171158 bases of 2818974548 (69.890%) in intersection + sed -e 's/^/ # /;' fb.mm10.chainSynGCF_036323735.1Link.txt + # 1838771241 bases of 2818974548 (65.228%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.chrom.sizes.txt" \ + \ + mm10 GCF_036323735.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 369m39.895s + + sed -e 's/^/ # /;' fb.mm10.chainRBest.GCF_036323735.1.txt + # 1762553574 bases of 2818974548 (62.525%) in intersection + +real 2795m19.421s +user 0m2.775s +sys 0m1.686s + +##############################################################################