src/hg/makeDb/doc/mm9.txt 1.101
1.101 2009/07/02 22:21:44 hiram
Rerun all the equCab2 chains and nets to clean up problems
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.100
retrieving revision 1.101
diff -b -B -U 4 -r1.100 -r1.101
--- src/hg/makeDb/doc/mm9.txt 29 Jun 2009 23:19:15 -0000 1.100
+++ src/hg/makeDb/doc/mm9.txt 2 Jul 2009 22:21:44 -0000 1.101
@@ -9423,4 +9423,58 @@
# The previous version had 493 miRNAs.
hgsql -e 'select count(distinct name) from miRNA;' mm9
# 541
# The previous version had 466 unique miRNAs.
+
+############################################################################
+# Re-Run equCab2 alignment (DONE - 2009-06-29,07-02 - Hiram
+ mkdir /hive/data/genomes/mm9/bed/lastzEquCab2.2009-06-29
+ cd /hive/data/genomes/mm9/bed/lastzEquCab2.2009-06-29
+
+ cat << '_EOF_' > DEF
+# Mouse vs. Horse
+
+BLASTZ_M=50
+
+# TARGET: Mouse MM9
+SEQ1_DIR=/scratch/data/mm9/nib
+SEQ1_LEN=/scratch/data/mm9/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/mm9/bed/lastzEquCab2.2009-06-29
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # real 360m10.094s
+ time doBlastzChainNet.pl `pwd`/DEF \
+ -continue=chainMerge -noLoadChainSplit -verbose=2 -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > chainMerge.log 2>&1 &
+ # real 225m4.178s
+ 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
+
+############################################################################