src/hg/makeDb/doc/danRer6.txt 1.6
1.6 2009/08/06 21:30:46 galt
chainSelf
Index: src/hg/makeDb/doc/danRer6.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/danRer6.txt,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/makeDb/doc/danRer6.txt 23 Jul 2009 19:12:38 -0000 1.5
+++ src/hg/makeDb/doc/danRer6.txt 6 Aug 2009 21:30:46 -0000 1.6
@@ -359,11 +359,11 @@
blat danRer6.2bit /dev/null /dev/null -tileSize=11 -makeOoc=11.ooc -repMatch=405
#Wrote 71088 overused 11-mers to 11.ooc
mkdir /hive/data/staging/data/danRer6
- cp -p danRer6.2bit /hive/data/staging/data/danRer6
- cp -p 11.ooc /hive/data/staging/data/danRer6
- cp -p chrom.sizes /hive/data/staging/data/danRer6
+ cp -p danRer6.2bit /hive/data/staging/data/danRer6/
+ cp -p 11.ooc /hive/data/staging/data/danRer6/
+ cp -p chrom.sizes /hive/data/staging/data/danRer6/
# ask admin to sync this directory: /hive/data/staging/data/danRer6/
# to the kluster nodes /scratch/data/danRer6/
@@ -621,10 +621,10 @@
# create lift file on unBridged gaps for genbank splits (2009-07-07 - Hiram)
mkdir /hive/data/genomes/danRer6/bed/gap
cd /hive/data/genomes/danRer6/bed/gap
gapToLift danRer6 danRer6.unBridged.lift -bedFile=unBridged.lift.bed
- cp -p danRer6.unBridged.lift ../../jkStuff
- cp -p danRer6.unBridged.lift /hive/data/staging/data/danRer6
+ cp -p danRer6.unBridged.lift ../../jkStuff/
+ cp -p danRer6.unBridged.lift /hive/data/staging/data/danRer6/
# ask admin to sync this directory: /hive/data/staging/data/danRer6/
# to the kluster nodes /scratch/data/danRer6/
@@ -715,5 +715,103 @@
# /hive/data/genomes/danRer6/goldenPath/database/README.txt
# /hive/data/genomes/danRer6/goldenPath/bigZips/README.txt
# (The htdocs/goldenPath/danRer6/*/README.txt "files" are just links to those.)
+############################################################################
+# Make Self Chain (WORKING - 2008-07-23)
+
+ ssh hgwdev
+
+ mkdir /hive/data/genomes/danRer6/bed/lastzSelf.2009-07-30
+ cd /hive/data/genomes/danRer6/bed/lastzSelf.2009-07-30
+
+ twoBitInfo ../../danRer6.2bit stdout | grep chr > chromOnly.len
+
+ cat << '_EOF_' > DEF
+# zebrafish vs self
+BLASTZ=lastz
+# maximum M allowed with lastz is only 254
+BLASTZ_M=254
+# lastz does not like the O= and E= lines in the matrix file
+# this copy has that removed from /scratch/data/scratch/human_chimp.v2.q
+BLASTZ_Q=/hive/data/genomes/hg19/bed/lastzHg19Haps.2009-03-09/human_chimp.v2.q
+# and place those items here
+BLASTZ_O=600
+BLASTZ_E=150
+# other parameters from hg18 vs venter1 lastz on advice from Webb
+BLASTZ_K=10000
+BLASTZ_Y=15000
+BLASTZ_T=2
+
+BASE=/hive/data/genomes/danRer6/bed/lastzSelf.2009-07-30
+
+# TARGET: Zebrafish danRer6
+SEQ1_DIR=/scratch/data/danRer6/danRer6.2bit
+SEQ1_LEN=$BASE/chromOnly.len
+SEQ1_CHUNK=10000000
+SEQ1_LAP=10000
+SEQ1_IN_CONTIGS=0
+
+# QUERY: Zebrafish danRer6
+SEQ2_DIR=/scratch/data/danRer6/danRer6.2bit
+SEQ2_LEN=$BASE/chromOnly.len
+SEQ2_CHUNK=10000000
+SEQ2_LAP=0
+SEQ2_IN_CONTIGS=0
+
+TMPDIR=/scratch/tmp
+'_EOF_'
+
+ screen # use screen to manage this long-running job
+ cd /hive/data/genomes/danRer6/bed/lastzSelf.2009-07-30
+ time nice doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+ -noLoadChainSplit -chainMinScore=2000 -chainLinearGap=medium \
+ -workhorse=hgwdev \
+ -stop=net -smallClusterHub=memk -bigClusterHub=swarm >& do.log &
+ # This took 26 hours to finish.
+
+ time nice doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+ -noLoadChainSplit -chainMinScore=2000 -chainLinearGap=medium \
+ -continue=load -debug -workhorse=hgwdev \
+ -stop=load -smallClusterHub=memk -bigClusterHub=swarm >& load.debug.log &
+
+ # load.debug.log indicates load step would do
+ # axtChain/loadUp.csh which would do:
+ # hgLoadChain -tIndex danRer6 chainSelf danRer6.danRer6.all.chain.gz
+
+ # Manually include the -normScore parameter for self-chains.
+ cd /hive/data/genomes/danRer6/bed/lastzSelf.2009-07-30/axtChain
+ hgLoadChain -normScore -tIndex danRer6 chainSelf danRer6.danRer6.all.chain.gz
+
+ # FYI For self-chains, we don't need to do the other steps
+ # that doBlastzChainNet.pl would normally do.
+
+ # add to zebrafish/danRer6/trackDb.ra
+track chainSelf
+shortLabel Self Chain
+longLabel Self Chained Alignments
+group varRep
+chromosomes
+chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chrM
+priority 400
+visibility hide
+color 100,50,0
+altColor 255,240,200
+chainColor Normalized Score
+spectrum on
+type chain danRer6
+otherDb danRer6
+
+
+
+#######################################################################
+# Finish danRer6.2bit in downloads (done 2009-07-31)
+#
+# NOTE this should not need to be done in future
+# because Hiram added the functionality to makeDownloads.pl
+#
+ ssh hgwdev
+ cd /hive/data/genomes/danRer6/
+ ln -s /hive/data/genomes/danRer6/danRer6.2bit /usr/local/apache/htdocs/goldenPath/danRer6/bigZips/
+ vi README
+ md5sum danRer6.2bit >> /usr/local/apache/htdocs/goldenPath/danRer6/bigZips/md5sum.txt