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 4 -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
@@ -91,4 +91,45 @@
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
+