8bdac6f85746594c3f307aa7bf1933cb84d43d3d hiram Thu Jan 19 13:08:53 2023 -0800 liftOver to GCF_016772045.1_ARS-UI_Ramb_v2.0 per user request refs #30517 diff --git src/hg/makeDb/doc/oviAri1.txt src/hg/makeDb/doc/oviAri1.txt index fc865c8..e6da5f7 100644 --- src/hg/makeDb/doc/oviAri1.txt +++ src/hg/makeDb/doc/oviAri1.txt @@ -720,16 +720,90 @@ cd /hive/data/genomes/oviAri1/bed/blat.oviAri3.2013-06-19 # check it with -debug first to see if it is going to work: doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=swarm \ -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \ -debug -dbHost=hgwdev -workhorse=hgwdev oviAri1 oviAri3 # if that is OK, then run it: time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=swarm \ -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \ -dbHost=hgwdev -workhorse=hgwdev oviAri1 oviAri3 > do.log 2>&1 # real 106m33.304s # verify this file exists: # /gbdb/oviAri1/liftOver/oviAri1ToOviAri3.over.chain.gz # and try out the conversion on genome-test from oviAri1 to oviAri3 -############################################################################ +############################################################################## +# LIFTOVER TO GCF_016772045.1_ARS-UI_Ramb_v2.0 (WORKING - 2023-01-19 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/oviAri1/bed/blat.GCF_016772045.1.2023-01-19 + cd /hive/data/genomes/oviAri1/bed/blat.GCF_016772045.1.2023-01-19 + doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \ + -targetSizes=/hive/data/genomes/oviAri1/chrom.sizes \ + -query2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \ + -querySizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \ + -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \ + oviAri1 GCF_016772045.1 + time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \ + -targetSizes=/hive/data/genomes/oviAri1/chrom.sizes \ + -query2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \ + -querySizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \ + -ooc=/hive/data/genomes/oviAri1/jkStuff/oviAri1.11.ooc \ + oviAri1 GCF_016772045.1) > doLiftOverToGCF_016772045.1.log 2>&1 +XXX - running - Thu Jan 19 13:08:03 PST 2023 + + # see if the liftOver menus function in the browser from oviAri1 + # to GCF_016772045.1 + +############################################################################## +# LIFTOVER TO oviAri1 (WORKING - 2023-01-19 - Hiram) + ssh hgwdev + # going to need an ooc for this GenArk hub + cd /hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0 + + # what is the 'real' size of this genome (without gaps): + head -1 *.faSize.txt +# 2628146905 bases (42000 N's 2628104905 real 1396540621 upper 1231564284 lower) +# in 142 sequences in 1 files + # note the 'real' size is 2628104905 + # ratio to standard human size: 2861349177 + # from: featureBits -noRandom -noHap hg19 gap + + calc \( 2628104905 / 2861349177 \) \* 1024 + # ( 2628104905 / 2861349177 ) * 1024 = 940.528141 + # round repMatch up to 1000 + + time blat GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit /dev/null /dev/null -tileSize=11 \ + -makeOoc=GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc -repMatch=1000 + + # should be a 'reasonable' number of 11-mers (10,000 to 30,000 or so) +# Wrote 28017 overused 11-mers to GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc +# real 0m24.648s + + mkdir /hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/blat.oviAri1.2023-01-19 + cd /hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/trackData/blat.oviAri1.2023-01-19 + doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \ + -targetSizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \ + -query2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \ + -querySizes=/hive/data/genomes/oviAri1/chrom.sizes \ + -ooc=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc \ + GCF_016772045.1 oviAri1 + time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -target2Bit=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.2bit \ + -targetSizes=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.chrom.sizes \ + -query2Bit=/hive/data/genomes/oviAri1/oviAri1.2bit \ + -querySizes=/hive/data/genomes/oviAri1/chrom.sizes \ + -ooc=/hive/data/genomes/asmHubs/refseqBuild/GCF/016/772/045/GCF_016772045.1_ARS-UI_Ramb_v2.0/GCF_016772045.1_ARS-UI_Ramb_v2.0.11.ooc \ + GCF_016772045.1 oviAri1) > doLiftOverToOviAri1.log 2>&1 +XXX - running - Thu Jan 19 13:08:03 PST 2023 + + # see if the liftOver menus function in the browser from oviAri1 + # to GCF_016772045.1 + +##############################################################################