src/hg/makeDb/doc/hg18.txt 1.367
1.367 2009/07/02 22:21:44 hiram
Rerun all the equCab2 chains and nets to clean up problems
Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.366
retrieving revision 1.367
diff -b -B -U 4 -r1.366 -r1.367
--- src/hg/makeDb/doc/hg18.txt 25 Jun 2009 18:15:15 -0000 1.366
+++ src/hg/makeDb/doc/hg18.txt 2 Jul 2009 22:21:44 -0000 1.367
@@ -28291,4 +28291,61 @@
print "$Chr\t$start\t$pos\t$value\n";
close(IN);
}
+############################################################################
+# Re-Run equCab2 alignment (DONE - 2009-06-29,07-02 - Hiram)
+ mkdir /hive/data/genomes/hg18/bed/lastzEquCab2.2009-06-29
+ cd /hive/data/genomes/hg18/bed/lastzEquCab2.2009-06-29
+
+ cat << '_EOF_' > DEF
+# Human vs. Horse
+
+BLASTZ_M=50
+
+# TARGET: Human hg18
+SEQ1_DIR=/scratch/data/hg18/bothMaskedNibs
+SEQ1_LEN=/scratch/data/hg18/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Horse
+SEQ2_DIR=/scratch/data/equCab2/equCab2.2bit
+SEQ2_LEN=/scratch/data/equCab2/chrom.sizes
+SEQ2_CTGDIR=/hive/data/genomes/equCab2/equCab2.UnScaffolds.2bit
+SEQ2_CTGLEN=/hive/data/genomes/equCab2/equCab2.UnScaffolds.sizes
+SEQ2_LIFT=/hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=100
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg18/bed/lastzEquCab2.2009-06-29
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 582m47.015s
+ # failed due to power failure - Mon Jun 29 23:32:54 PDT 2009
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -continue=chainRun -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > chainRun.log 2>&1 &
+ # real 430m13.886s
+ cat fb.hg18.chainEquCab2Link.txt
+ # 1647122438 bases of 2881515245 (57.162%) in intersection
+
+ mkdir /hive/data/genomes/equCab2/bed/blastz.hg18.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.hg18.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/hg18/bed/lastzEquCab2.2009-06-29/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -swap -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 238m42.004s
+ cat fb.equCab2.chainHg18Link.txt
+ # 1622340736 bases of 2428790173 (66.796%) in intersection
+
+############################################################################