src/hg/makeDb/doc/hg19.txt 1.25

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 4 -r1.24 -r1.25
--- src/hg/makeDb/doc/hg19.txt	7 Jun 2009 23:47:50 -0000	1.24
+++ src/hg/makeDb/doc/hg19.txt	11 Jun 2009 18:17:32 -0000	1.25
@@ -4284,5 +4284,96 @@
   -chainMinScore=3000 -chainLinearGap=medium -swap cavPor3.DEF >& cavPor3.doSwap.log
 # [detach screen]
 real    192m39.792s
 
-##########################################################################
+
+
+##############################################################################
+# LASTZ Sea Hare aplCal1 (STARTING - 2009-06-08 - Galt)
+    mkdir /hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08
+    cd /hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08
+
+    cat << '_EOF_' > DEF
+# Human vs. Sea Hare
+BLASTZ_Y=3400
+BLASTZ_L=6000
+BLASTZ_K=2200
+BLASTZ_M=50
+BLASTZ_Q=/scratch/data/blastz/HoxD55.q
+
+# TARGET: Human Hg19
+SEQ1_DIR=/scratch/data/hg19/hg19.2bit
+SEQ1_LEN=/scratch/data/hg19/chrom.sizes
+SEQ1_CHUNK=100000000
+SEQ1_LAP=10000
+SEQ2_LIMIT=5
+
+# QUERY: Sea Hare aplCal1
+SEQ2_DIR=/scratch/data/aplCal1/aplCal1.2bit
+SEQ2_LEN=/scratch/data/aplCal1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=300
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08
+TMPDIR=/scratch/tmp
+'_EOF_'
+    # << happy emacs
+
+    #	establish a screen to control this job
+    #   (NOTE I SHOULD NOT HAVE USED  -qRepeats=windowmaskerSdust)
+    screen
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+	`pwd`/DEF \
+	-qRepeats=windowmaskerSdust \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+	>& do.log &
+    #	real ?? about one hour but one job hung
+
+    # resuming from failure 
+    # edited loadUp.csh, commenting out the first completed step
+    # and removing the unneeded -qRepeats=windowmaskerSdust
+    # from the next step, now run it to complete the load step.
+    /hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08/axtChain/loadUp.csh \ 
+        >& continue-loadUp.log&
+
+    # continue from step 'download'
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+        `pwd`/DEF \
+        -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+        -continue download \
+        >& continue-download.log &
+ 
+    cat fb.hg19.chainAplCal1Link.txt 
+    #   19675762 bases of 2897316137 (0.679%) in intersection
+
+    #	running the swap - DONE - 2009-06-02
+    #   (NOTE I SHOULD NOT HAVE USED  -qRepeats=windowmaskerSdust)
+    mkdir /hive/data/genomes/aplCal1/bed/blastz.hg19.swap
+    cd /hive/data/genomes/aplCal1/bed/blastz.hg19.swap
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08/DEF \
+	-qRepeats=windowmaskerSdust \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+	-swap >& swap.log &
+    #	real  time not long
+
+    # resuming from failure
+    # edited loadUp.csh, commenting out the first completed step
+    # and removing the unneeded -tRepeats=windowmaskerSdust
+    # from the next step, now run it to complete the load step.
+    /hive/data/genomes/aplCal1/bed/blastz.hg19.swap/axtChain/loadUp.csh \
+        >& continue-loadUp.log&
+
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/hg19/bed/lastzAplCal1.2009-06-08/DEF \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+	-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+        -continue download \
+	-swap >& continue-download.log &
+
+    cat fb.aplCal1.chainHg19Link.txt 
+    #   14163455 bases of 619228098 (2.287%) in intersection
+