86ae147ac68707dcb81a697e5e45f4619465097e hiram Tue Feb 16 08:52:47 2021 -0800 completed lastz/chain/net to mm10 mm39 hg38 for rn7 release refs #26682 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index a2860b8..39b4df7 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -291,56 +291,55 @@ # establish a screen to control this job screen -S mm39Rn7 time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 & # real 364m51.738s sed -e 's/^/ # /;' fb.mm39.chainRn7Link.txt # 1898735724 bases of 2654624157 (71.526%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynRn7Link.txt # 1787593557 bases of 2654624157 (67.339%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ mm39 rn7) > rbest.log 2>&1 & -XXX - running - Fri Feb 5 11:01:26 PST 2021 - # real 580m33.404s + # real 588m38.122s + sed -e 's/^/ # /;' fb.mm39.chainRBest.Rn7.txt - # 1738608299 bases of 2654624157 (65.494%) in intersection + # 1754204799 bases of 2654624157 (66.081%) in intersection mkdir /hive/data/genomes/rn7/bed/blastz.mm39.swap cd /hive/data/genomes/rn7/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 # real 116m47.862s sed -e 's/^/ # /;' fb.rn7.chainMm39Link.txt # 1855165978 bases of 2626580772 (70.630%) in intersection sed -e 's/^/ # /;' fb.rn7.chainSynMm39Link.txt # 1763550257 bases of 2626580772 (67.142%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ rn7 mm39) > rbest.log 2>&1 -XXX - running - Fri Feb 5 11:00:02 PST 2021 - # real 675m42.654s + # real 605m42.354s sed -e 's/^/ # /;' fb.rn7.chainRBest.Mm39.txt - # 1740516499 bases of 2729860805 (63.758%) in intersection + # 1754416686 bases of 2626580772 (66.795%) in intersection ############################################################################## # LASTZ Chinese hamster criGriChoV2 (DONE - 2020-11-23 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23 cd /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23 printf '# Chinese hamster vs Mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Chinese hamster CriGriChoV2