src/hg/makeDb/doc/oviAri1.txt 1.6
1.6 2010/05/06 16:27:44 chinhli
Lastz finished
Index: src/hg/makeDb/doc/oviAri1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/oviAri1.txt,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/makeDb/doc/oviAri1.txt 27 Apr 2010 19:30:46 -0000 1.5
+++ src/hg/makeDb/doc/oviAri1.txt 6 May 2010 16:27:44 -0000 1.6
@@ -465,26 +465,8 @@
tcsh
cd /hive/data/genomes/bosTau4/bed/lastzOviAri1.2010-04-16/axtChain
./netSynteny.csh > & netSynteny_tcsh.log
-==== begin pig ==========
- # and the swap
- mkdir /hive/data/genomes/bosTau4/bed/blastz.oviAri1.swap
- cd /hive/data/genomes/bosTau4/bed/blastz.oviAri1.swap
- time nice -n +19 doBlastzChainNet.pl -verbose=2 \
- /hive/data/genomes/oviAri1/bed/lastzBosTau4.2010-03-27/DEF \
- -swap -noLoadChainSplit -syntenicNet \
- -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
- -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
- # most interesting, this failed on the first step chainSwap
- # but the failure didn't make it stop, it continued and produced
- # zero results to the end. Running manually:
- cd /hive/data/genomes/bosTau4/bed/blastz.oviAri1.swap/axtChain
-export sizeG=188743680
-ulimit -d $sizeG
-ulimit -v $sizeG
-
-======== end pig =======
# and the swap
mkdir /hive/data/genomes/oviAri1/bed/blastz.bosTau4.swap
cd /hive/data/genomes/oviAri1/bed/blastz.bosTau4.swap
@@ -540,8 +522,10 @@
# original alignment
cd /hive/data/genomes/monDom5/bed/lastzOviAri1.2010-04-16
cat fb.monDom5.chainOviAri1Link.txt
# 133534458 bases of 3501660299 (3.813%) in intersection
+ cd /hive/data/genomes/monDom5/bed/
+ ln -s lastzFelCatV17e.2010-03-22 lastz.oviAri1
# and the swap
mkdir /hive/data/genomes/oviAri1/bed/blastz.monDom5.swap
cd /hive/data/genomes/oviAri1/bed/blastz.monDom5.swap
@@ -576,9 +560,9 @@
cat fb.oviAri1.chainEquCab2Link.txt
# 940763026 bases of 1201271277 (78.314%) in intersection
############################################################################
-# running cpgIsland business (DONE - 2010-03-31 - Hiram)
+# running cpgIsland business (DONE -2010-04-29 - Chin)
mkdir /hive/data/genomes/oviAri1/bed/cpgIsland
cd /hive/data/genomes/oviAri1/bed/cpgIsland
cvs -d /projects/compbio/cvsroot checkout -P hg3rdParty/cpgIslands
cd hg3rdParty/cpgIslands
@@ -626,19 +610,30 @@
endif
'_EOF_'
# << happy emacs
+ chmod 775 runOne
gensub2 chr.list single template jobList
para create jobList
para try
para check ... etc
para time
-# Completed: 20 of 20 jobs
-# CPU time in finished jobs: 168s 2.79m 0.05h 0.00d 0.000 y
-# IO & Wait Time: 86s 1.44m 0.02h 0.00d 0.000 y
-# Average job time: 13s 0.21m 0.00h 0.00d
-# Longest finished job: 29s 0.48m 0.01h 0.00d
-# Submission to last job: 31s 0.52m 0.01h 0.00d
+ para problems
+ para status
+ # then, kick it with para push
+ # check it with plb
+ # when all are done, para time shows:
+ # para time
+ # 1218 jobs in batch
+ # 319 jobs (including everybody's) in Parasol queue or running.
+ # Checking finished jobs
+ # Completed: 1218 of 1218 jobs
+ # CPU time in finished jobs: 201s 3.36m 0.06h 0.00d 0.000 y
+ # IO & Wait Time: 3099s 51.64m 0.86h 0.04d 0.000 y
+ # Average job time: 3s 0.05m 0.00h 0.00d
+ # Longest finished job: 25s 0.42m 0.01h 0.00d
+ # Submission to last job: 90s 1.50m 0.03h 0.00d
+ # Estimated complete: 0s 0.00m 0.00h 0.00d
# Transform cpglh output to bed +
catDir results | awk '{
$2 = $2 - 1;
@@ -651,15 +646,20 @@
ssh hgwdev
cd /hive/data/genomes/oviAri1/bed/cpgIsland
hgLoadBed oviAri1 cpgIslandExt -tab \
-sqlTable=$HOME/kent/src/hg/lib/cpgIslandExt.sql cpgIsland.bed
- # Loaded 38778 elements of size 10
+ # Loaded 25384 elements of size 10
+ # Sorted
+ # Creating table definition for cpgIslandExt
+ # Saving bed.tab
+ # Loading oviAri1
+
# cleanup
rm -fr hardMaskedFa
#########################################################################
-# all.joiner update, downloads and in pushQ - (DONE - 2010-03-31 - Hiram)
+# all.joiner update, downloads and in pushQ - (??? Pending the ISg status 2010-04-29)
cd $HOME/kent/src/hg/makeDb/schema
# fixup all.joiner until this is a clean output
joinerCheck -database=oviAri1 -all all.joiner