5fbb00b2cc364c5a543b26825e5db67f4fa6d9e1 hiram Thu Jan 19 12:33:54 2023 -0800 liftOver to GCA_001632575.1 per user request refs #30492 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 1cd4c7a..632e98a 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -18619,20 +18619,82 @@ # 2272307441 bases of 2588619290 (87.781%) in intersection sed -e 's/^/ # /;' fb.GCA_001624535.1.chainSynMm10Link.txt # 2258459310 bases of 2588619290 (87.246%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/535/GCA_001624535.1/GCA_001624535.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/535/GCA_001624535.1/GCA_001624535.1.chrom.sizes.txt" \ GCA_001624535.1 mm10) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 93m42.796s sed -e 's/^/ # /;' fb.GCA_001624535.1.chainRBest.Mm10.txt # 2255354454 bases of 2588619290 (87.126%) in intersection -############################################################################## real 1211m31.498s user 0m1.396s sys 0m1.411s +############################################################################## + +############################################################################## +# LIFTOVER TO GCA_001632575.1_C3H_HeJ_v1 (WORKING - 2023-01-19 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/mm10/bed/blat.GCA_001632575.1.2023-01-19 + cd /hive/data/genomes/mm10/bed/blat.GCA_001632575.1.2023-01-19 + doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -targetSizes=/hive/data/genomes/mm10/chrom.sizes \ + -query2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \ + -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \ + -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \ + mm10 GCA_001632575.1 + time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -targetSizes=/hive/data/genomes/mm10/chrom.sizes \ + -query2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \ + -querySizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \ + -ooc=/hive/data/genomes/mm10/jkStuff/mm10.11.ooc \ + mm10 GCA_001632575.1) > doLiftOverToGCA_001632575.1.log 2>&1 +XXX - running - Thu Jan 19 12:32:47 PST 2023 + + # see if the liftOver menus function in the browser from mm10 + # to GCA_001632575.1 + +############################################################################## +# LIFTOVER TO mm10 (WORKING - 2023-01-19 - Hiram) + ssh hgwdev + # going to need an ooc for this GenArk hub + cd /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1 + time blat GCA_001632575.1_C3H_HeJ_v1.2bit /dev/null /dev/null -tileSize=11 \ + -makeOoc=GCA_001632575.1_C3H_HeJ_v1.11.ooc -repMatch=1000 +# Wrote 14128 overused 11-mers to GCA_001632575.1_C3H_HeJ_v1.11.ooc +# real 0m46.685s + + + mkdir /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blat.mm10.2023-01-19 + cd /hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/trackData/blat.mm10.2023-01-19 + doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \ + -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \ + -query2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -querySizes=/hive/data/genomes/mm10/chrom.sizes \ + -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.11.ooc \ + GCA_001632575.1 mm10 + time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.2bit \ + -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.chrom.sizes \ + -query2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -querySizes=/hive/data/genomes/mm10/chrom.sizes \ + -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/632/575/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.11.ooc \ + GCA_001632575.1 mm10) > doLiftOverToMm10.log 2>&1 +XXX - running - Thu Jan 19 12:32:47 PST 2023 + + # see if the liftOver menus function in the browser from mm10 + # to GCA_001632575.1 + +##############################################################################