src/hg/makeDb/doc/monDom5.txt 1.17
1.17 2010/01/25 19:16:13 hiram
panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig
Index: src/hg/makeDb/doc/monDom5.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/monDom5.txt,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 4 -r1.16 -r1.17
--- src/hg/makeDb/doc/monDom5.txt 28 Sep 2009 20:49:09 -0000 1.16
+++ src/hg/makeDb/doc/monDom5.txt 25 Jan 2010 19:16:13 -0000 1.17
@@ -1439,5 +1439,99 @@
#Submission to last job: 343s 5.72m 0.10h 0.00d
## Stitch up wig files, make .wibs, load in DB
+############################################################################
+# susScr1 Pig BLASTZ/CHAIN/NET (DONE - 2010-01-21,22 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/monDom5/bed/lastzSusScr1.2010-01-21
+ cd /hive/data/genomes/monDom5/bed/lastzSusScr1.2010-01-21
+ cat << '_EOF_' > DEF
+# Pig vs. Opossum
+BLASTZ_M=50
+
+# TARGET: Opossum MonDom5
+SEQ1_DIR=/scratch/data/monDom5/monDom5.2bit
+SEQ1_LEN=/scratch/data/monDom5/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Pig SusScr1
+SEQ2_DIR=/scratch/data/susScr1/susScr1.2bit
+SEQ2_LEN=/scratch/data/susScr1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/monDom5/bed/lastzSusScr1.2010-01-21
+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=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
+ # real 992m51.260s
+ cat fb.monDom5.chainSusScr1Link.txt
+ # 179898391 bases of 3501660299 (5.138%) in intersection
+
+ mkdir /hive/data/genomes/susScr1/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/susScr1/bed/blastz.monDom5.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/monDom5/bed/lastzSusScr1.2010-01-21/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # real 97m35.156s
+ cat fb.susScr1.chainMonDom5Link.txt
+ # 182834626 bases of 2231332019 (8.194%) in intersection
+
+#########################################################################
+# ailMel1 Panda BLASTZ/CHAIN/NET (DONE - 2010-01-22 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
+ cd /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
+
+ cat << '_EOF_' > DEF
+# Panda vs. Opossum
+BLASTZ_M=50
+
+# TARGET: Opossum MonDom5
+SEQ1_DIR=/scratch/data/monDom5/monDom5.2bit
+SEQ1_LEN=/scratch/data/monDom5/chrom.sizes
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+
+# QUERY: Panda AilMel1
+SEQ2_DIR=/scratch/data/ailMel1/ailMel1.2bit
+SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22
+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=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > do.log 2>&1 &
+ # real 293m25.573s
+ cat fb.monDom5.chainAilMel1Link.txt
+ # 223233047 bases of 3501660299 (6.375%) in intersection
+
+ mkdir /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-01-22/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # real 65m0.711s
+ cat fb.ailMel1.chainMonDom5Link.txt
+ # 210235815 bases of 2225124764 (9.448%) in intersection
+
+#########################################################################