src/hg/makeDb/doc/bosTau4.txt 1.23

Index: src/hg/makeDb/doc/bosTau4.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/bosTau4.txt,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/hg/makeDb/doc/bosTau4.txt	25 Jan 2010 19:16:14 -0000	1.22
+++ src/hg/makeDb/doc/bosTau4.txt	1 Apr 2010 17:33:10 -0000	1.23
@@ -1828,12 +1828,12 @@
     md5sum bosTau4ToBosTauMd3.over.chain.gz >> md5sum.txt
     popd
 
 #########################################################################
-# susScr1 Pig BLASTZ/CHAIN/NET (WORKING - 2010-01-21 - Hiram)
+# susScr1 Pig BLASTZ/CHAIN/NET (DONE - 2010-01-25 - Hiram)
     screen # use a screen to manage this multi-day job
-    mkdir /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
-    cd /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
+    mkdir /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-25
+    cd /hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-25
 
     cat << '_EOF_' > DEF
 # Pig vs. Cow
 BLASTZ_M=50
@@ -1850,21 +1850,26 @@
 SEQ2_LEN=/scratch/data/susScr1/chrom.sizes
 SEQ2_CHUNK=10000000
 SEQ2_LAP=0
 
-BASE=/hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-21
+BASE=/hive/data/genomes/bosTau4/bed/lastzSusScr1.2010-01-25
 TMPDIR=/scratch/tmp
 '_EOF_'
     # << this line keeps emacs coloring happy
 
     time nice -n +19 doBlastzChainNet.pl -verbose=2 \
 	`pwd`/DEF \
 	-noLoadChainSplit -syntenicNet \
-	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
 	-chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+    #	real    2377m21.473s
+    #	never did get this to work.  susScr2 as target bosTau4 as query
+    #	did finish but with immense chain pileups
+    #	failed second time too
+    #	XXX - re-running as 01-25 (was 01-21) Mon Jan 25 11:29:32 PST 2010
     #	real    3811m31.428s
     #	failed
-XXX - running Thu Jan 21 14:49:43 PST 2010
+    #	XXX - running Thu Jan 25 14:49:43 PST 2010
 
     time nice -n +19 $HOME/kent/src/hg/utils/automation/doBlastzChainNet.pl \
 	`pwd`/DEF -verbose=2 \
 	-bigClusterHub=memk -chainMinScore=3000 -chainLinearGap=medium \
@@ -1888,4 +1893,52 @@
     cat fb.bosTau4.chainRn4Link.txt 
     #	664253901 bases of 2731830700 (24.315%) in intersection
 
 #########################################################################
+# lastz swap Pig SusScr2 (DONE - 2010-03-31 - Hiram)
+    #	the primary lastz run on susScr2
+    cd /hive/data/genomes/susScr2/bed/lastzBosTau4.2010-03-27
+    cat fb.susScr2.chainBosTau4Link.txt 
+    #	1478903080 bases of 2231298548 (66.280%) in intersection
+
+    #	and the swap
+    mkdir /hive/data/genomes/bosTau4/bed/blastz.susScr2.swap
+    cd /hive/data/genomes/bosTau4/bed/blastz.susScr2.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/susScr2/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.susScr2.swap/axtChain
+export sizeG=188743680
+ulimit -d $sizeG
+ulimit -v $sizeG
+
+chainSwap /hive/data/genomes/susScr2/bed/lastzBosTau4.2010-03-27/axtChain/susScr2.bosTau4.all.chain.gz stdout \
+| nice chainSort stdin stdout | nice gzip -c > bosTau4.susScr2.all.chain.gz
+
+    #	it also runs out of memory in the lift over file creation:
+    export sizeG=188743680
+    ulimit -d $sizeG
+    ulimit -v $sizeG
+
+    netChainSubset -verbose=0 noClass.net bosTau4.susScr2.all.chain.gz stdout \
+	| chainStitchId stdin stdout | gzip -c > bosTau4.susScr2.over.chain.gz
+
+    #	and netChains.csh is finished manually with this added:
+# memory limit 160 Gb
+limit datasize 163840m
+limit vmemoryuse 163840m
+
+    #	manually run the loadUp.csh with this added:
+# memory limit 160 Gb
+limit datasize 163840m
+limit vmemoryuse 163840m
+    #	real    498m5.861s
+
+    cat fb.bosTau4.chainSusScr2Link.txt
+    #	1383557633 bases of 2731830700 (50.646%) in intersection
+
+#########################################################################