c3fdad60d8f01da6ff3296b216015ebae858b06c hiram Fri May 29 17:12:51 2020 -0700 continue lastz/chain/net run for user refs #25625 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 31631bb..2476208 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -17695,58 +17695,81 @@ # 737924732 bases of 2481941580 (29.732%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev canFam4 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 173m38.016s cat fb.canFam4.chainRBest.Mm10.txt # 740357755 bases of 2481941580 (29.830%) in intersection ############################################################################## # LASTZ woodchuck/Marmota monax/GCA_901343595.1 (DONE - 2020-05-29 - Hiram) # establish a screen to control this job mkdir /hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29 cd /hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29 + # do NOT want dots in the name of the sequence, eliminate the .1 -> v1 + ln -s /hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/GCA_901343595.1_MONAX5.2bit GCA_901343595v1_MONAX5.2bit + ln -s /hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/GCA_901343595.1_MONAX5.chrom.sizes GCA_901343595v1_MONAX5.chrom.sizes + printf '# woodchuck/Marmota monax/GCA_901343595.1 vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_M=254 # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: woodchuck/Marmota monax/GCA_901343595.1 -SEQ2_DIR=/hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/GCA_901343595.1_MONAX5.2bit -SEQ2_LEN=/hive/data/genomes/asmHubs/genbankBuild/GCA/901/343/595/GCA_901343595.1_MONAX5/GCA_901343595.1_MONAX5.chrom.sizes +SEQ2_DIR=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit +SEQ2_LEN=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=400 SEQ2_LAP=0 BASE=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -noDbNameCheck -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & -XXX - running - Fri May 29 11:19:19 PDT 2020 +XXX - running - Fri May 29 17:11:31 PDT 2020 + # real 98m5.996s + + # slight problem with the resulting chain table name: + # chainGCA_901343595.1_MONAX5 + # can not have a table name with .1 like that, MySQL thought + # that was database chainGCA_901343595 taable 1_MONAX5 + # fixed up loadUp.csh to do that correctly with name: + # chainGCA_901343595v1_MONAX5 + # would need to change the SEQ2_DIR name + # make some symLinks and have settings: +# SEQ2_DIR=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.2bit +# SEQ2_LEN=/hive/data/genomes/mm10/bed/lastzGCA_901343595v1.2020-05-29/GCA_901343595v1_MONAX5.chrom.sizes # real 483m10.607s + time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ + -continue=download -noDbNameCheck -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > download.log 2>&1 & + + cat fb.mm10.chainGCA_901343595v1_MONAX5Link.txt + # 923698956 bases of 2652783500 (34.820%) in intersection cat fb.mm10.chainCanFam4Link.txt # 777883731 bases of 2652783500 (29.323%) in intersection cat fb.mm10.chainSynCanFam4Link.txt # 736602602 bases of 2652783500 (27.767%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev mm10 canFam4 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 219m16.168s cat fb.mm10.chainRBest.CanFam4.txt # 741307883 bases of 2652783500 (27.945%) in intersection mkdir /hive/data/genomes/canFam4/bed/blastz.mm10.swap