src/hg/makeDb/doc/mm9.txt 1.130
1.130 2010/03/29 16:01:26 hiram
done with susScr2 lastz and swap
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.129
retrieving revision 1.130
diff -b -B -U 4 -r1.129 -r1.130
--- src/hg/makeDb/doc/mm9.txt 25 Mar 2010 18:24:48 -0000 1.129
+++ src/hg/makeDb/doc/mm9.txt 29 Mar 2010 16:01:26 -0000 1.130
@@ -5777,9 +5777,9 @@
> rbest.log 2>&1 &
# real 27m3.076s
#########################################################################
-## 30-Way Multiz (WORKING - 2007-10-01 - Hiram)
+## 30-Way Multiz (DONE - 2007-10-01 - Hiram)
## The blastz alignments for this 30-way are documented at:
## http://genomewiki.ucsc.edu/index.php/Mm9_multiple_alignment
##
ssh hgwdev
@@ -6160,9 +6160,9 @@
# real 30m26.542s
#############################################################################
## Annotate 30-way multiple alignment with gene annotations
-## (WORKING - 2007-10-18 - Hiram)
+## (DONE - 2007-10-18 - Hiram)
# Gene frames
## survey all genomes to see what type of gene track to use
ssh hgwdev
mkdir /cluster/data/mm9/bed/multiz30way/frames
@@ -6330,9 +6330,9 @@
# frames multiz30wayFrames
# irows on
#############################################################################
-# phastCons 30-way (WORKING - 2007-10-16 - Hiram)
+# phastCons 30-way (DONE - 2007-10-16 - Hiram)
# split 30way mafs into 10M chunks and generate sufficient statistics
# files for # phastCons
ssh kki
@@ -10046,9 +10046,9 @@
cat fb.ailMel1.chainMm9Link.txt
# 739076250 bases of 2245312831 (32.916%) in intersection
############################################################################
-# susScr1 Pig BLASTZ/CHAIN/NET (WORKING - 2010-01-21 - Hiram)
+# 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/mm9/bed/lastzSusScr1.2010-01-21
cd /hive/data/genomes/mm9/bed/lastzSusScr1.2010-01-21
@@ -10223,4 +10223,51 @@
cat fb.calJac3.chainHg19Link.txt
# 861811978 bases of 2752505800 (31.310%) in intersection
#####################################################################
+# susScr2 Pig BLASTZ/CHAIN/NET (DONE - 2010-03-26,27 - Hiram)
+ screen # use a screen to manage this multi-day job
+ mkdir /hive/data/genomes/mm9/bed/lastzSusScr2.2010-03-26
+ cd /hive/data/genomes/mm9/bed/lastzSusScr2.2010-03-26
+
+ cat << '_EOF_' > DEF
+# Pig vs. Mouse
+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: Pig SusScr2
+SEQ2_DIR=/scratch/data/susScr2/susScr2.2bit
+SEQ2_LEN=/scratch/data/susScr2/chrom.sizes
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/mm9/bed/lastzSusScr2.2010-03-26
+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=encodek -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1 &
+ # Elapsed time: 717m25s
+ cat fb.mm9.chainSusScr2Link.txt
+ # 616615408 bases of 2620346127 (23.532%) in intersection
+
+ mkdir /hive/data/genomes/susScr2/bed/blastz.mm9.swap
+ cd /hive/data/genomes/susScr2/bed/blastz.mm9.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/mm9/bed/lastzSusScr2.2010-03-26/DEF \
+ -swap -noLoadChainSplit -syntenicNet \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # Elapsed time: 63m4s
+ cat fb.susScr2.chainMm9Link.txt
+ # 656444411 bases of 2231298548 (29.420%) in intersection
+
+############################################################################