src/hg/makeDb/doc/ailMel1.txt 1.2
1.2 2009/12/26 06:09:30 hiram
ready for genbank run
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
+