db2c189b474c037cb383b96c06b71acdcf364dd7 hiram Sun Mar 2 17:56:46 2025 -0800 lastz chainNet procedures for xenTro10 refs #31490 diff --git src/hg/makeDb/doc/xenTro10/lastzChainNet.txt src/hg/makeDb/doc/xenTro10/lastzChainNet.txt new file mode 100644 index 00000000000..1b4677080cb --- /dev/null +++ src/hg/makeDb/doc/xenTro10/lastzChainNet.txt @@ -0,0 +1,504 @@ +############################################################################## +# LASTZ Peter's clawed frog GCA_038501915.1 vs. X. tropicalis XenTro10 +# (DONE - 2025-02-13 - hiram) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13 + cd /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13 + + printf '# X. tropicalis XenTro10 vs. Peter's clawed frog GCA_038501915.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Peter's clawed frog 2024-04-29 GCA_038501915.1_aXenPet1.maternal.cur +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: X. tropicalis xenTro10 +SEQ2_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ2_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_038501915.1_aXenPet1.maternal.cur -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 1480m29.005s + + sed -e 's/^/ # /;' fb.GCA_038501915.1.chainXenTro10Link.txt + # 1083830546 bases of 2613116200 (41.477%) in intersection + sed -e 's/^/ # /;' fb.GCA_038501915.1.chainSynXenTro10Link.txt + # 765321850 bases of 2613116200 (29.288%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt" \ + \ + GCA_038501915.1 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1606m26.757s + + sed -e 's/^/ # /;' fb.GCA_038501915.1.chainRBest.XenTro10.txt + # 576881473 bases of 2613116200 (22.076%) in intersection + + ### and for the swap + + cd /hive/data/genomes/xenTro10/bed/blastz.GCA_038501915.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_038501915.1_aXenPet1.maternal.cur /hive/data/genomes/asmHubs/allBuild/GCA/038/501/915/GCA_038501915.1_aXenPet1.maternal.cur/trackData/lastzXenTro10.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 395m19.938s + + sed -e 's/^/ # /;' fb.xenTro10.chainGCA_038501915.1Link.txt + # 764127358 bases of 1451301209 (52.651%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynGCA_038501915.1Link.txt + # 440012956 bases of 1451301209 (30.319%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/038/501/915/GCA_038501915.1/GCA_038501915.1.chrom.sizes.txt" \ + \ + xenTro10 GCA_038501915.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1205m48.958s + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.GCA_038501915.1.txt + # 560732929 bases of 1451301209 (38.637%) in intersection + +############################################################################## + +real 4688m8.748s +user 0m4.677s +sys 0m1.347s +############################################################################## +# LASTZ Tungara frog GCA_040894015.1 vs. X. tropicalis XenTro10 +# (DONE - 2025-02-13 - hiram) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13 + cd /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13 + + printf '# X. tropicalis XenTro10 vs. Tungara frog GCA_040894015.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Tungara frog 2024-07-30 GCA_040894015.1_aEngPut4.paternal +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: X. tropicalis xenTro10 +SEQ2_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ2_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_040894015.1_aEngPut4.paternal -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 999m15.041s + + sed -e 's/^/ # /;' fb.GCA_040894015.1.chainXenTro10Link.txt + # 133488473 bases of 2081032022 (6.415%) in intersection + sed -e 's/^/ # /;' fb.GCA_040894015.1.chainSynXenTro10Link.txt + # 68568592 bases of 2081032022 (3.295%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt" \ + \ + GCA_040894015.1 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 160m38.277s + + sed -e 's/^/ # /;' fb.GCA_040894015.1.chainRBest.XenTro10.txt + # 87644098 bases of 2081032022 (4.212%) in intersection + + ### and for the swap + + cd /hive/data/genomes/xenTro10/bed/blastz.GCA_040894015.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_040894015.1_aEngPut4.paternal /hive/data/genomes/asmHubs/allBuild/GCA/040/894/015/GCA_040894015.1_aEngPut4.paternal/trackData/lastzXenTro10.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 11m31.922s + + sed -e 's/^/ # /;' fb.xenTro10.chainGCA_040894015.1Link.txt + # 127498005 bases of 1451301209 (8.785%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynGCA_040894015.1Link.txt + # 68364702 bases of 1451301209 (4.711%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/040/894/015/GCA_040894015.1/GCA_040894015.1.chrom.sizes.txt" \ + \ + xenTro10 GCA_040894015.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 130m14.716s + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.GCA_040894015.1.txt + # 86980009 bases of 1451301209 (5.993%) in intersection + +############################################################################## + +real 1301m43.127s +user 0m4.023s +sys 0m1.174s +############################################################################## +# LASTZ X. tropicalis XenTro10 vs. zebrafish GCF_000002035.6 +# (DONE - 2025-02-13 - hiram) + + mkdir /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13 + cd /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13 + + printf '# zebrafish GCF_000002035.6 vs. X. tropicalis XenTro10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: X. tropicalis xenTro10 +SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: zebrafish 2017-05-09 GCF_000002035.6_GRCz11 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_000002035.6_GRCz11 -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 997m10.494s + + sed -e 's/^/ # /;' fb.xenTro10.chainGCF_000002035.6Link.txt + # 49497650 bases of 1451301209 (3.411%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynGCF_000002035.6Link.txt + # 6978571 bases of 1451301209 (0.481%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt" \ + xenTro10 GCF_000002035.6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 63m43.386s + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.GCF_000002035.6.txt + # 28398632 bases of 1451301209 (1.957%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/002/035/GCF_000002035.6_GRCz11/trackData/blastz.xenTro10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_000002035.6_GRCz11 /hive/data/genomes/xenTro10/bed/lastzGCF_000002035.6.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 4m7.885s + + sed -e 's/^/ # /;' fb.GCF_000002035.6.chainXenTro10Link.txt + # 49866746 bases of 1679203469 (2.970%) in intersection + sed -e 's/^/ # /;' fb.GCF_000002035.6.chainSynXenTro10Link.txt + # 8305312 bases of 1679203469 (0.495%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/002/035/GCF_000002035.6/GCF_000002035.6.chrom.sizes.txt" \ + GCF_000002035.6 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 68m54.720s + + sed -e 's/^/ # /;' fb.GCF_000002035.6.chainRBest.XenTro10.txt + # 28571626 bases of 1679203469 (1.701%) in intersection + +############################################################################## + +real 1133m59.601s +user 0m3.890s +sys 0m1.493s +############################################################################## +# LASTZ X. tropicalis XenTro10 vs. African clawed frog GCF_017654675.1 +# (DONE - 2025-02-26 - hiram) + + mkdir /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13 + cd /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13 + + printf '# African clawed frog GCF_017654675.1 vs. X. tropicalis XenTro10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: X. tropicalis xenTro10 +SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: African clawed frog 2021-04-12 GCF_017654675.1_Xenopus_laevis_v10.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_017654675.1_Xenopus_laevis_v10.1 -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 1107m12.745s + + sed -e 's/^/ # /;' fb.xenTro10.chainGCF_017654675.1Link.txt + # 787548572 bases of 1451301209 (54.265%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynGCF_017654675.1Link.txt + # 453079461 bases of 1451301209 (31.219%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt" \ + xenTro10 GCF_017654675.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.GCF_017654675.1.txt + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/017/654/675/GCF_017654675.1_Xenopus_laevis_v10.1/trackData/blastz.xenTro10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_017654675.1_Xenopus_laevis_v10.1 /hive/data/genomes/xenTro10/bed/lastzGCF_017654675.1.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 627m20.150s + + sed -e 's/^/ # /;' fb.GCF_017654675.1.chainXenTro10Link.txt + # 1159922816 bases of 2742469346 (42.295%) in intersection + sed -e 's/^/ # /;' fb.GCF_017654675.1.chainSynXenTro10Link.txt + # 831958092 bases of 2742469346 (30.336%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/017/654/675/GCF_017654675.1/GCF_017654675.1.chrom.sizes.txt" \ + GCF_017654675.1 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 2253m11.082s + + sed -e 's/^/ # /;' fb.GCF_017654675.1.chainRBest.XenTro10.txt + # 604418262 bases of 2742469346 (22.039%) in intersection + +############################################################################## + +real 2880m34.676s +user 0m2.816s +sys 0m0.974s +############################################################################## +# LASTZ X. tropicalis XenTro10 vs. Lizard AnoCar2 +# (DONE - 2025-02-13 - hiram) + + mkdir /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13 + cd /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13 + + printf '# Lizard AnoCar2 vs. X. tropicalis XenTro10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: X. tropicalis xenTro10 +SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Lizard anoCar2 +SEQ2_DIR=/hive/data/genomes/anoCar2/anoCar2.2bit +SEQ2_LEN=/hive/data/genomes/anoCar2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ + -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 1001m2.254s + + sed -e 's/^/ # /;' fb.xenTro10.chainAnoCar2Link.txt + # 46493232 bases of 1448461978 (3.210%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynAnoCar2Link.txt + # 23478176 bases of 1448461978 (1.621%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + xenTro10 anoCar2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 54m20.733s + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.AnoCar2.txt + # 34957007 bases of 1448461978 (2.413%) in intersection + + ### and for the swap + + cd /hive/data/genomes/anoCar2/bed/blastz.xenTro10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/xenTro10/bed/lastzAnoCar2.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 4m41.713s + + sed -e 's/^/ # /;' fb.anoCar2.chainXenTro10Link.txt + # 40831822 bases of 1701353770 (2.400%) in intersection + sed -e 's/^/ # /;' fb.anoCar2.chainSynXenTro10Link.txt + # 22681746 bases of 1701353770 (1.333%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + anoCar2 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 51m45.564s + + sed -e 's/^/ # /;' fb.anoCar2.chainRBest.XenTro10.txt + # 34961125 bases of 1701353770 (2.055%) in intersection + +############################################################################## + +real 1111m50.936s +user 0m3.159s +sys 0m0.749s +############################################################################## +# LASTZ X. tropicalis XenTro10 vs. Chicken GalGal6 +# (DONE - 2025-02-13 - hiram) + + mkdir /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13 + cd /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13 + + printf '# Chicken GalGal6 vs. X. tropicalis XenTro10 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: X. tropicalis xenTro10 +SEQ1_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit +SEQ1_LEN=/hive/data/genomes/xenTro10/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Chicken galGal6 +SEQ2_DIR=/hive/data/genomes/galGal6/galGal6.2bit +SEQ2_LEN=/hive/data/genomes/galGal6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ + -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 1000m18.466s + + sed -e 's/^/ # /;' fb.xenTro10.chainGalGal6Link.txt + # 50287701 bases of 1448461978 (3.472%) in intersection + sed -e 's/^/ # /;' fb.xenTro10.chainSynGalGal6Link.txt + # 31107843 bases of 1448461978 (2.148%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + xenTro10 galGal6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 40m0.991s + + sed -e 's/^/ # /;' fb.xenTro10.chainRBest.GalGal6.txt + # 37686782 bases of 1448461978 (2.602%) in intersection + + ### and for the swap + + cd /hive/data/genomes/galGal6/bed/blastz.xenTro10.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ + /hive/data/genomes/xenTro10/bed/lastzGalGal6.2025-02-13/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 3m47.069s + + sed -e 's/^/ # /;' fb.galGal6.chainXenTro10Link.txt + # 40888835 bases of 1055588482 (3.874%) in intersection + sed -e 's/^/ # /;' fb.galGal6.chainSynXenTro10Link.txt + # 30606958 bases of 1055588482 (2.900%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + \ + galGal6 xenTro10) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 29m33.510s + + sed -e 's/^/ # /;' fb.galGal6.chainRBest.XenTro10.txt + # 37557937 bases of 1055588482 (3.558%) in intersection + +############################################################################## + +real 1073m40.468s +user 0m3.180s +sys 0m0.639s