0b1eaa046425cf42843abc6fd9fbf4a7e2d696a0 mspeir Mon Apr 7 09:22:03 2025 -0700 adding several alignments, refs #35465 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index ef048be1651..fb1d408b3b9 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -3627,15 +3627,181 @@ -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 ############################################################################## +# LASTZ chicken GCF_016699485.2 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-03-29 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGCF_002263795.3.2025-03-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGCF_002263795.3.2025-03-29 + + printf '# domestic cattle GCF_002263795.3 vs. chicken GCF_016699485.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: chicken 2021-01-19 GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/699/485/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b/trackData/lastzGCF_002263795.3.2025-03-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 529m17.551s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainGCF_002263795.3Link.txt + # 65747596 bases of 1053332251 (6.242%) in intersection + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainSynGCF_002263795.3Link.txt + # 56491753 bases of 1053332251 (5.363%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/699/485/GCF_016699485.2/GCF_016699485.2.chrom.sizes.txt" \ + -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" \ + GCF_016699485.2 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 31m3.421s + + sed -e 's/^/ # /;' fb.GCF_016699485.2.chainRBest.GCF_002263795.3.txt + # 61370569 bases of 1053332251 (5.826%) in intersection + +real 608m55.656s +user 0m3.549s +sys 0m4.420s + +############################################################################## +# LASTZ water buffalo GCF_019923935.1 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-03-29 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_002263795.3.2025-03-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_002263795.3.2025-03-29 + + printf '# domestic cattle GCF_002263795.3 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: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +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/lastzGCF_002263795.3.2025-03-29 +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 -qAsmId GCF_002263795.3_ARS-UCD2.0 -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 1391m18.793s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainGCF_002263795.3Link.txt + # 2523561371 bases of 2622460639 (96.229%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynGCF_002263795.3Link.txt + # 2484937936 bases of 2622460639 (94.756%) 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" \ + -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" \ + GCF_019923935.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 121m39.232s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.GCF_002263795.3.txt + # 2477606886 bases of 2622460639 (94.476%) in intersection + +real 2188m28.175s +user 0m3.562s +sys 0m3.507s + +############################################################################## +# LASTZ pig GCF_000003025.6 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-04-01 - mspeir) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/trackData/lastzGCF_002263795.3.2025-04-01 + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/trackData/lastzGCF_002263795.3.2025-04-01 + + printf '# domestic cattle GCF_002263795.3 vs. pig GCF_000003025.6 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: pig 2017-02-07 GCF_000003025.6_Sscrofa11.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/000/003/025/GCF_000003025.6_Sscrofa11.1/trackData/lastzGCF_002263795.3.2025-04-01 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_000003025.6_Sscrofa11.1 -qAsmId GCF_002263795.3_ARS-UCD2.0 -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 1517m50.926s + + sed -e 's/^/ # /;' fb.GCF_000003025.6.chainGCF_002263795.3Link.txt + # 1537487649 bases of 2501912388 (61.452%) in intersection + sed -e 's/^/ # /;' fb.GCF_000003025.6.chainSynGCF_002263795.3Link.txt + # 1457737528 bases of 2501912388 (58.265%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.chrom.sizes.txt" \ + -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" \ + GCF_000003025.6 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 273m18.460s + +real 2275m33.144s +user 0m3.060s +sys 0m3.413s