Index: src/hg/makeDb/doc/ailMel1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ailMel1.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/makeDb/doc/ailMel1.txt	23 Dec 2009 22:54:57 -0000	1.1
+++ src/hg/makeDb/doc/ailMel1.txt	26 Dec 2009 06:09:30 -0000	1.2
@@ -1,94 +1,135 @@
 # for emacs: -*- mode: sh; -*-
 
 #	$Id$
 
 # Panda sequence: http://panda.genomics.org.cn/page/panda/download.jsp
 #	Ailuropoda melanoleuca
 
 ##########################################################################
 # Download sequence (DONE - 2009-12-17 - Hiram)
     mkdir /hive/data/genomes/ailMel1
     cd /hive/data/genomes/ailMel1
     mkdir download
     cd download
 
 wget --timestamping \
 'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
 
 wget --timestamping \
 'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda_contig100.mapping_scaffolds_nucmer.list.clean.tab.sort.gff.gz'
 
 wget --timestamping \
 'ftp://panda.genomics.org.cn/pub/panda/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
 
 
     faCount panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz > faCount.txt
 
     grep "^scaff" faCount.txt | awk '{print $1}' > scaffold.list
 
     faSomeRecords panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz \
 	scaffold.list stdout | gzip > scaffolds.fa.gz
 
     hgFakeAgp scaffolds.fa.gz stdout | sed -e "s/D/W/" > fake.agp
 
 ##########################################################################
 # Initial genome build (DONE - 2009-12-17 - Hiram)
     cd /hive/data/genomes/ailMel1
 
     cat << '_EOF_' > ailMel1.config.ra
 # Config parameters for makeGenomeDb.pl:
 db ailMel1
 clade mammal
 genomeCladePriority 19
 scientificName Ailuropoda melanoleuca
 commonName Panda
 assemblyDate Dec. 2009
 assemblyLabel BGI-Shenzhen AilMel 1.0 Dec. 2009
 orderKey 220
 mitoAcc NC_009492
 fastaFiles /hive/data/genomes/ailMel1/download/scaffolds.fa.gz
 agpFiles /hive/data/genomes/ailMel1/download/fake.agp
 # qualFiles none
 dbDbSpeciesDir panda
 taxId 9646
 
     makeGenomeDb.pl -stop=seq ailMel1.config.ra > seq.out 2>&1
     makeGenomeDb.pl -start=agp -stop=agp ailMel1.config.ra > agp.out 2>&1
     makeGenomeDb.pl -start=db -stop=db ailMel1.config.ra > db.out 2>&1
     makeGenomeDb.pl -start=dbDb -stop=dbDb ailMel1.config.ra > dbDb.out 2>&1
     makeGenomeDb.pl -start=trackDb -stop=trackDb ailMel1.config.ra > trackDb.out 2>&1
 
 ##########################################################################
 # running repeat masker (DONE - 2009-12-21 - Hiram)
     mkdir /hive/data/genomes/ailMel1/bed/repeatMasker
     cd /hive/data/genomes/ailMel1/bed/repeatMasker
     doRepeatMasker.pl -buildDir=`pwd` -noSplit -bigClusterHub=swarm \
 	-workhorse=hgwdev ailMel > do.log 2>&1
     cat faSize.rmsk.txt
 # 2279048486 bases (54196431 N's 2224852055 real 1356361826 upper
 #	868490229 lower) in 12195 sequences in 1 files
 # %38.11 masked total, %39.04 masked real
 
 ##########################################################################
 # running simple repeat (DONE - 2009-12-21 - Hiram)
     mkdir /hive/data/genomes/ailMel1/bed/simpleRepeat
     cd /hive/data/genomes/ailMel1/bed/simpleRepeat
     doSimpleRepeat.pl -buildDir=`pwd` -smallClusterHub=swarm \
 	-workhorse=hgwdev ailMel > do.log 2>&1
 
     cat fb.simpleRepeat 
 # 24968229 bases of 2225124764 (1.122%) in intersection
 
     twoBitMask ailMel1.rmsk.2bit \
 	-add bed/simpleRepeat/trfMask.bed ailMel1.2bit
     #	you can safely ignore the warning about fields >= 13
 
     twoBitToFa ailMel1.2bit stdout | faSize stdin > faSize.ailMel1.2bit.txt
     cat faSize.ailMel1.2bit.txt
 # 2279048486 bases (54196431 N's 2224852055 real 1355773543 upper
 #	869078512 lower) in 12195 sequences in 1 files
 # %38.13 masked total, %39.06 masked real
     rm /gbdb/ailMel1/ailMel1.2bit
     ln -s `pwd`/ailMel1.2bit /gbdb/ailMel1/ailMel1.2bit
 
 ##########################################################################
+#  BLATSERVERS ENTRY (DONE - 2009-12-23 - Hiram)
+#	After getting a blat server assigned by the Blat Server Gods,
+    ssh hgwdev
+
+    hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+	VALUES ("ailMel1", "blat12", "17802", "1", "0"); \
+	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+	VALUES ("ailMel1", "blat12", "17803", "0", "1");' \
+	    hgcentraltest
+    #	test it with some sequence
+
+#########################################################################
+# MAKE 11.OOC FILES FOR BLAT (DONE - 2009-12-23 - Hiram)
+    ssh kolossus
+    # numerator is ailMel1 gapless bases as reported by faSize 
+    # denominator is hg17 gapless bases as reported by featureBits,
+    # 1024 is threshold used for human -repMatch:
+    calc \( 2224852055 / 2897310462 \) \* 1024
+# ( 2224852055 / 2897310462 ) * 1024 = 786.332198
+    # ==> use -repMatch=750 according to size scaled down from 1024 for human.
+    #	and rounded down to nearest 50
+    cd /hive/data/genomes/ailMel1
+    blat ailMel1.2bit /dev/null /dev/null -tileSize=11 \
+      -makeOoc=jkStuff/ailMel1.11.ooc -repMatch=750
+    #	Wrote 25042 overused 11-mers to jkStuff/ailMel1.11.ooc
+
+    mkdir /hive/data/staging/data/ailMel
+    cp -p ailMel1.2bit chrom.sizes jkStuff/ailMel1.11.ooc \
+	/hive/data/staging/data/ailMel1
+
+
+#########################################################################
+# genbank run
+    time nice -n +19 bin/gbAlignStep -initial  ailMel1 &
+
+    logFile: var/build/logs/2009.12.24-15:03:26.ailMel1.initalign.log
+
+ nice ./bin/gbDbLoadStep -drop -initialLoad ailMel1 &
+[1] 10050
+[hiram@hgwdev /cluster/data/genbank] logFile: var/dbload/hgwdev/logs/2009.12.25-00:08:46.dbload.log
+

