src/hg/makeDb/doc/loxAfr3.txt 1.3
1.3 2009/07/23 15:14:50 braney
added human proteins track
Index: src/hg/makeDb/doc/loxAfr3.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/loxAfr3.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 4 -r1.2 -r1.3
--- src/hg/makeDb/doc/loxAfr3.txt 23 Jul 2009 00:53:28 -0000 1.2
+++ src/hg/makeDb/doc/loxAfr3.txt 23 Jul 2009 15:14:50 -0000 1.3
@@ -140,9 +140,9 @@
cvs ci -m "Added loxAfr3 - Loxodonta africana" etc/align.dbs etc/hgwdev.dbs
make etc-update
##########################################################################
-# HUMAN (hg18) PROTEINS TRACK (started 2009-07-22 braney )
+# HUMAN (hg18) PROTEINS TRACK (DONE 2009-07-23 braney )
# bash if not using bash shell already
cd /cluster/data/loxAfr3
mkdir /cluster/data/loxAfr3/blastDb
@@ -240,14 +240,14 @@
para create blastSpec
# para try, check, push, check etc.
para time
-# Completed: 251158 of 251158 jobs
-# CPU time in finished jobs: 8587545s 143125.76m 2385.43h 99.39d 0.272 y
-# IO & Wait Time: 885281s 14754.68m 245.91h 10.25d 0.028 y
-# Average job time: 38s 0.63m 0.01h 0.00d
-# Longest finished job: 1167s 19.45m 0.32h 0.01d
-# Submission to last job: 9852s 164.20m 2.74h 0.11d
+# Completed: 251776 of 251776 jobs
+# CPU time in finished jobs: 18571030s 309517.16m 5158.62h 214.94d 0.589 y
+# IO & Wait Time: 1488748s 24812.47m 413.54h 17.23d 0.047 y
+# Average job time: 80s 1.33m 0.02h 0.00d
+# Longest finished job: 287s 4.78m 0.08h 0.00d
+# Submission to last job: 21050s 350.83m 5.85h 0.24d
ssh swarm
cd /cluster/data/loxAfr3/bed/tblastn.hg18KG
mkdir chainRun
@@ -268,15 +268,14 @@
# do the cluster run for chaining
para create chainSpec
para try, check, push, check etc.
-# Completed: 166 of 166 jobs
-# CPU time in finished jobs: 107801s 1796.69m 29.94h 1.25d 0.003 y
-# IO & Wait Time: 23945s 399.08m 6.65h 0.28d 0.001 y
-# Average job time: 794s 13.23m 0.22h 0.01d
-# Longest finished job: 25056s 417.60m 6.96h 0.29d
-# Submission to last job: 25085s 418.08m 6.97h 0.29d
-
+# Completed: 64 of 64 jobs
+# CPU time in finished jobs: 29478s 491.30m 8.19h 0.34d 0.001 y
+# IO & Wait Time: 19822s 330.37m 5.51h 0.23d 0.001 y
+# Average job time: 770s 12.84m 0.21h 0.01d
+# Longest finished job: 2868s 47.80m 0.80h 0.03d
+# Submission to last job: 2882s 48.03m 0.80h 0.03d
cd /cluster/data/loxAfr3/bed/tblastn.hg18KG/blastOut
for i in kg??
do
@@ -296,11 +295,10 @@
hgLoadPsl loxAfr3 blastHg18KG.psl
# check coverage
featureBits loxAfr3 blastHg18KG
-# 19115900 bases of 1506896106 (1.269%) in intersection
-
- featureBits loxAfr3 blastHg18KG refGene -enrichment
-# blastHg18KG 1.269%, refGene 1.827%, both 0.659%, cover 51.97%, enrich 28.45x
+# 42480830 bases of 3118565340 (1.362%) in intersection
+ featureBits loxAfr3 blastHg18KG xenoRefGene -enrichment
+# blastHg18KG 1.362%, xenoRefGene 1.615%, both 0.695%, cover 51.03%, enrich 31.60x
rm -rf blastOut
#end tblastn