src/hg/makeDb/doc/hg18.txt 1.345
1.345 2009/02/12 22:42:29 kate
Add primate and glire lineage specific phyloP
Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.344
retrieving revision 1.345
diff -b -B -U 4 -r1.344 -r1.345
--- src/hg/makeDb/doc/hg18.txt 3 Feb 2009 07:11:40 -0000 1.344
+++ src/hg/makeDb/doc/hg18.txt 12 Feb 2009 22:42:29 -0000 1.345
@@ -26140,9 +26140,9 @@
#Converted stdin, upper limit 0.99, lower limit -8.17
ln -s /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP/primate/wig/phyloP44wayPrimate.wib /gbdb/hg18/multiz44way/phyloP44wayPrimate.wib
hgLoadWiggle -pathPrefix=/gbdb/hg18/multiz44way hg18 phyloP44wayPrimate phyloP44wayPrimate.wig
- # get stats
+# get stats
cd run.phyloP/all
hgWiggle -db=hg18 -verbose=2 -doStats phyloP44wayAll > stats.out
hgWiggle -db=hg18 -chr=chr20 -rawDataOut phyloP44wayAll | textHistogram -real stdin -minVal=-20 -maxBinCount=30 >&! histo.out
@@ -26160,9 +26160,9 @@
# Downloads
cd /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP
cat > listWigsByChrom.csh << 'EOF'
- setee = $1
+ set c = $1
foreach d (`ls -d $c/[1-9]* | sort -t/ -k2 -n`)
ls -1 $d/*.wig | sort -n -t\. -k3
end
'EOF'
@@ -26175,9 +26175,8 @@
csh ../../listWigsByChrom.csh $c | xargs cat | gzip -c > ../downloads/$c.$1.wigFix.gz
end
cd ../downloads
md5sum *.wigFix.gz > md5sum.txt
- end
'EOF'
cd all/wig
csh ../../downloads.csh phyloP44way >&! downloads.log &
@@ -26235,12 +26234,53 @@
para try
para check
para push
- # Mostly crashes -- sending error to Adam
- # GOT HERE
+ para time
+#CPU time in finished jobs: 4949300s 82488.33m 1374.81h 57.28d 0.157 y
+#IO & Wait Time: 143956s 2399.27m 39.99h 1.67d 0.005 y
+#Average job time: 1805s 30.08m 0.50h 0.02d
+#Longest finished job: 2780s 46.33m 0.77h 0.03d
+#Submission to last job: 6447s 107.45m 1.79h 0.07d
+
+ # process results and load wiggle
+ ssh hgwdev
+ cd /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP/primate-ls/wig
+ csh ../../listWig.csh | xargs cat | nice wigEncode stdin phyloP44wayPrimateLs.wig phyloP44wayPrimateLs.wib
+ #Converted stdin, upper limit 3.91, lower limit -9.28
+ ln -s /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP/primate-ls/wig/phyloP44wayPrimateLs.wib /gbdb/hg18/multiz44way/phyloP44wayPrimateLs.wib
+ hgLoadWiggle -pathPrefix=/gbdb/hg18/multiz44way hg18 phyloP44wayPrimateLs phyloP44wayPrimateLs.wig
+
+ # glire lineage-specfic
+ cd /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP
+ mkdir glire-ls
+ cd glire-ls
+ cp ../../../4d/44way.all-ancestors.mod tree.mod
+ mkdir wig
+ sed 's/SUBTREE/mm9-oryCun1/' ../template.subtree > template.ls
+ gensub2 ../in.list single template.ls jobList
+ para create jobList
+ # 2823 jobs
+ para try
+ para check
+ para push
+
+ para time
+ #CPU time in finished jobs: 5173192s 86219.87m 1437.00h 59.87d 0.164 y
+ #IO & Wait Time: 145615s 2426.91m 40.45h 1.69d 0.005 y
+ #Average job time: 1884s 31.40m 0.52h 0.02d
+ #Longest finished job: 2721s 45.35m 0.76h 0.03d
+ #Submission to last job: 6883s 114.72m 1.91h 0.08d
+
+ # process results and load wiggle
+ ssh hgwdev
+ cd /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP/glire-ls/wig
+ csh ../../listWig.csh | xargs cat | nice wigEncode stdin phyloP44wayGlireLs.wig phyloP44wayGlireLs.wib
+ #Converted stdin, upper limit 5.95, lower limit -6.99
+
+ ln -s /cluster/data/hg18/bed/multiz44way/consPhyloP/run.phyloP/glire-ls/wig/phyloP44wayGlireLs.wib /gbdb/hg18/multiz44way/phyloP44wayGlireLs.wib
+ hgLoadWiggle -pathPrefix=/gbdb/hg18/multiz44way hg18 phyloP44wayGlireLs phyloP44wayGlireLs.wig
- #human LS: --subtree hg18
######################################################################
# downloads for 44-way (DONE - 2009-01-09 - Hiram)
mkdir -p /hive/data/genomes/hg18/bed/multiz44way/downloads/maf