src/hg/makeDb/doc/susScr2.txt 1.7
1.7 2010/04/14 13:35:20 braney
finished Human Proteins
Index: src/hg/makeDb/doc/susScr2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/susScr2.txt,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/makeDb/doc/susScr2.txt 13 Apr 2010 23:13:32 -0000 1.6
+++ src/hg/makeDb/doc/susScr2.txt 14 Apr 2010 13:35:20 -0000 1.7
@@ -629,9 +629,9 @@
-workhorse=hgwdev \
-ooc=/hive/data/genomes/susScr1/jkStuff/susScr1.11.ooc \
susScr1 susScr2 > do.log 2>&1
#############################################################################
-# HUMAN (hg18) PROTEINS TRACK (working braney...)
+# HUMAN (hg18) PROTEINS TRACK (DONE braney 2010-04-14)
# bash if not using bash shell already
cd /cluster/data/susScr2
mkdir /cluster/data/susScr2/blastDb
@@ -652,34 +652,32 @@
/hive/data/outside/blast229/formatdb -i $i -p F
done
rm *.fa
ls *.nsq | wc -l
-# 3275
-
+# 2915
mkdir -p /cluster/data/susScr2/bed/tblastn.hg18KG
cd /cluster/data/susScr2/bed/tblastn.hg18KG
echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
wc -l query.lst
-# 3275 query.lst
+# 2915 query.lst
- # we want around 800000 jobs
- calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(800000/`wc query.lst | awk '{print $1}'`\)
+ # we want around 350000 jobs
+ calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(350000/`wc query.lst | awk '{print $1}'`\)
-# 36727/(800000/3275) = 150.351156
+# 36727/(350000/2915) = 305.883443
mkdir -p kgfa
- split -l 150 /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl kgfa/kg
+ split -l 306 /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl kgfa/kg
cd kgfa
for i in *; do
nice pslxToFa $i $i.fa;
rm $i;
done
cd ..
ls -1S kgfa/*.fa > kg.lst
wc kg.lst
-# 245 245 3185 kg.lst
-
+# 121 121 1573 kg.lst
mkdir -p blastOut
for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
tcsh
@@ -731,14 +729,15 @@
para create blastSpec
# para try, check, push, check etc.
para time
-# Completed: 802375 of 802375 jobs
-# CPU time in finished jobs: 17244679s 287411.32m 4790.19h 199.59d 0.547 y
-# IO & Wait Time: 4643016s 77383.60m 1289.73h 53.74d 0.147 y
-# Average job time: 27s 0.45m 0.01h 0.00d
-# Longest finished job: 164s 2.73m 0.05h 0.00d
-# Submission to last job: 45538s 758.97m 12.65h 0.53d
+# Completed: 352715 of 352715 jobs
+# CPU time in finished jobs: 13184770s 219746.16m 3662.44h 152.60d 0.418 y
+# IO & Wait Time: 1844130s 30735.51m 512.26h 21.34d 0.058 y
+# Average job time: 43s 0.71m 0.01h 0.00d
+# Longest finished job: 149s 2.48m 0.04h 0.00d
+# Submission to last job: 16902s 281.70m 4.70h 0.20d
+
ssh swarm
cd /cluster/data/susScr2/bed/tblastn.hg18KG
mkdir chainRun
@@ -759,14 +758,14 @@
# do the cluster run for chaining
para create chainSpec
para try, check, push, check etc.
-# Completed: 254 of 254 jobs
-# CPU time in finished jobs: 590077s 9834.62m 163.91h 6.83d 0.019 y
-# IO & Wait Time: 20749s 345.81m 5.76h 0.24d 0.001 y
-# Average job time: 2405s 40.08m 0.67h 0.03d
-# Longest finished job: 36592s 609.87m 10.16h 0.42d
-# Submission to last job: 36604s 610.07m 10.17h 0.42d
+# Completed: 121 of 121 jobs
+# CPU time in finished jobs: 342462s 5707.70m 95.13h 3.96d 0.011 y
+# IO & Wait Time: 67882s 1131.37m 18.86h 0.79d 0.002 y
+# Average job time: 3391s 56.52m 0.94h 0.04d
+# Longest finished job: 13532s 225.53m 3.76h 0.16d
+# Submission to last job: 13544s 225.73m 3.76h 0.16d
cd /cluster/data/susScr2/bed/tblastn.hg18KG/blastOut
for i in kg??
do
@@ -777,21 +776,20 @@
done
sort u.*.psl m60* | uniq | sort -T /tmp -k 14,14 -k 16,16n -k 17,17n > ../blastHg18KG.psl
cd ..
pslCheck blastHg18KG.psl
-# checked: 38517 failed: 0 errors: 0
+# checked: 83553 failed: 0 errors: 0
# load table
ssh hgwdev
cd /cluster/data/susScr2/bed/tblastn.hg18KG
hgLoadPsl susScr2 blastHg18KG.psl
# check coverage
featureBits susScr2 blastHg18KG
-# 18646943 bases of 332311746 (5.611%) in intersection
+# 36312685 bases of 2231298548 (1.627%) in intersection
featureBits susScr2 blastHg18KG ensGene -enrichment
-# blastHg18KG 5.611%, ensGene 9.520%, both 4.993%, cover 88.97%, enrich 9.35x
+# blastHg18KG 1.627%, ensGene 1.284%, both 0.845%, cover 51.91%, enrich 40.42x
rm -rf blastOut
#end tblastn
-}