src/hg/makeDb/doc/equCab2.txt 1.26
1.26 2009/07/02 22:21:45 hiram
Rerun all the equCab2 chains and nets to clean up problems
Index: src/hg/makeDb/doc/equCab2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/equCab2.txt,v
retrieving revision 1.25
retrieving revision 1.26
diff -b -B -U 4 -r1.25 -r1.26
--- src/hg/makeDb/doc/equCab2.txt 3 Dec 2008 01:05:20 -0000 1.25
+++ src/hg/makeDb/doc/equCab2.txt 2 Jul 2009 22:21:45 -0000 1.26
@@ -2207,4 +2207,145 @@
update equCab2.transMapAlnRefSeq set tSize=39960074 where tName="chr27" and tSize=65921033;
update equCab2.transMapAlnMRna set tSize=39960074 where tName="chr27" and tSize=65921033;
update equCab2.transMapAlnSplicedEst set tSize=39960074 where tName="chr27" and tSize=65921033;
+############################################################################
+# Re-Run GalGal3 lastz (DONE - 2009-07-01 - Hiram)
+ # primary run
+ cd /hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29
+ cat fb.galGal3.chainEquCab2Link.txt
+ # 68476046 bases of 1042591351 (6.568%) in intersection
+
+ # running the swap
+ mkdir /hive/data/genomes/equCab2/bed/blastz.galGal3.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.galGal3.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/galGal3/bed/lastzEquCab2.2009-06-29/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=pk \
+ -swap -workhorse=hgwdev \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 10m1.381s
+ cat fb.equCab2.chainGalGal3Link.txt
+ # 73336799 bases of 2428790173 (3.019%) in intersection
+
+############################################################################
+# Re-Run ornAna1 alignment (DONE - 2009-07-01,02 - Hiram)
+ mkdir /hive/data/genomes/equCab2/bed/lastzOrnAna1.2009-07-01
+ cd /hive/data/genomes/equCab2/bed/lastzOrnAna1.2009-07-01
+
+ cat << '_EOF_' > DEF
+# Horse vs. Platypus
+
+BLASTZ_M=50
+
+# TARGET: Horse
+SEQ1_DIR=/scratch/data/equCab2/equCab2.2bit
+SEQ1_LEN=/scratch/data/equCab2/chrom.sizes
+SEQ1_CTGDIR=/hive/data/genomes/equCab2/equCab2.UnScaffolds.2bit
+SEQ1_CTGLEN=/hive/data/genomes/equCab2/equCab2.UnScaffolds.sizes
+SEQ1_LIFT=/hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift
+SEQ1_CHUNK=20000000
+SEQ1_LIMIT=100
+SEQ1_LAP=0
+
+# QUERY: Platypus ornAna1
+SEQ2_DIR=/scratch/data/ornAna1/ornAna1.2bit
+SEQ2_LEN=/scratch/data/ornAna1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=400
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/equCab2/bed/lastzOrnAna1.2009-07-01
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -workhorse=hgwdev \
+ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
+ # real 1413m12.090s
+ cat fb.equCab2.chainOrnAna1Link.txt
+ # 132750149 bases of 2428790173 (5.466%) in intersection
+
+ mkdir /hive/data/genomes/ornAna1/bed/blastz.equCab2.swap
+ cd /hive/data/genomes/ornAna1/bed/blastz.equCab2.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/equCab2/bed/lastzOrnAna1.2009-07-01/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -swap -workhorse=hgwdev \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # real 115m47.611s
+ cat fb.ornAna1.chainEquCab2Link.txt
+ # 132776204 bases of 1842236818 (7.207%) in intersection
+
+############################################################################
+# lastz swap to Dog CanFam2 (DONE - 2009-07-01 - Hiram)
+ # the original lastz
+ cd /hive/data/genomes/canFam2/bed/lastzEquCab2.2009-06-29
+ cat fb.canFam2.chainEquCab2Link.txt
+ # 1676663178 bases of 2384996543 (70.300%) in intersection
+
+ mkdir /hive/data/genomes/equCab2/bed/blastz.canFam2.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.canFam2.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/canFam2/bed/lastzEquCab2.2009-06-29/DEF \
+ -swap -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 286m51.658s
+ fb.equCab2.chainCanFam2Link.txt
+ # 1721407500 bases of 2428790173 (70.875%) in intersection
+
+############################################################################
+# lastz swap to Mouse Mm9 (DONE - 2009-07-02 - Hiram)
+ # the original lastz
+ cd /hive/data/genomes/mm9/bed/lastzEquCab2.2009-06-29
+ cat fb.mm9.chainEquCab2Link.txt
+ # 912421053 bases of 2620346127 (34.821%) in intersection
+
+ mkdir /hive/data/genomes/equCab2/bed/blastz.mm9.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.mm9.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/mm9/bed/lastzEquCab2.2009-06-29/DEF \
+ -swap -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 122m25.314s
+ cat fb.equCab2.chainMm9Link.txt
+ # 902295813 bases of 2428790173 (37.150%) in intersection
+
+############################################################################
+# lastz swap to Opossum MonDom5 (DONE - 2009-07-02 - Hiram)
+ # the original lastz
+ cd /hive/data/genomes/monDom5/bed/lastzEquCab2.2009-06-29
+ cat fb.monDom5.chainEquCab2Link.txt
+ # 355004426 bases of 3501660299 (10.138%) in intersection
+
+ mkdir /hive/data/genomes/equCab2/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/equCab2/bed/blastz.monDom5.swap
+ time doBlastzChainNet.pl \
+ /hive/data/genomes/monDom5/bed/lastzEquCab2.2009-06-29/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -swap -workhorse=hgwdev \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # real 320m3.573s
+ cat fb.equCab2.chainMonDom5Link.txt
+ # 351787662 bases of 2428790173 (14.484%) in intersection
+
+#########################################################################
+# lastz swap to Human Hg18 (DONE - 2009-07-02 - Hiram)
+ # the original lastz
+ cd /hive/data/genomes/hg18/bed/lastzEquCab2.2009-06-29
+ 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
+
+############################################################################