src/hg/makeDb/doc/ailMel1.txt 1.13
1.13 2010/04/20 00:06:17 braney
added Human Proteins
Index: src/hg/makeDb/doc/ailMel1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ailMel1.txt,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 4 -r1.12 -r1.13
--- src/hg/makeDb/doc/ailMel1.txt 19 Apr 2010 17:03:46 -0000 1.12
+++ src/hg/makeDb/doc/ailMel1.txt 20 Apr 2010 00:06:17 -0000 1.13
@@ -414,9 +414,9 @@
cat fb.ailMel1.chainRn4Link.txt
# 695366144 bases of 2245312831 (30.970%) in intersection
#########################################################################
-# HUMAN (hg18) PROTEINS TRACK (working
+# HUMAN (hg18) PROTEINS TRACK (DONE braney 2010-04-19)
# bash if not using bash shell already
cd /cluster/data/ailMel1
mkdir /cluster/data/ailMel1/blastDb
@@ -437,32 +437,32 @@
/hive/data/outside/blast229/formatdb -i $i -p F
done
rm *.fa
ls *.nsq | wc -l
-# 2915
+# 2757
mkdir -p /cluster/data/ailMel1/bed/tblastn.hg18KG
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
wc -l query.lst
-# 2915 query.lst
+# 2757 query.lst
# 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/(350000/2915) = 305.883443
+# 36727/(350000/2757) = 289.303826
mkdir -p kgfa
- split -l 306 /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl kgfa/kg
+ split -l 289 /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
-# 121 121 1573 kg.lst
+# 128 128 1664 kg.lst
mkdir -p blastOut
for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
tcsh
@@ -514,15 +514,14 @@
para create blastSpec
# para try, check, push, check etc.
para time
-# 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
-
+# Completed: 352896 of 352896 jobs
+# CPU time in finished jobs: 13166354s 219439.24m 3657.32h 152.39d 0.418 y
+# IO & Wait Time: 1995282s 33254.69m 554.24h 23.09d 0.063 y
+# Average job time: 43s 0.72m 0.01h 0.00d
+# Longest finished job: 207s 3.45m 0.06h 0.00d
+# Submission to last job: 15726s 262.10m 4.37h 0.18d
ssh swarm
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
mkdir chainRun
@@ -543,14 +542,14 @@
# do the cluster run for chaining
para create chainSpec
para try, check, push, check etc.
-# 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
+# Completed: 128 of 128 jobs
+#CPU time in finished jobs: 1401s 23.35m 0.39h 0.02d 0.000 y
+#IO & Wait Time: 47407s 790.12m 13.17h 0.55d 0.002 y
+#Average job time: 381s 6.36m 0.11h 0.00d
+#Longest finished job: 466s 7.77m 0.13h 0.01d
+#Submission to last job: 470s 7.83m 0.13h 0.01d
cd /cluster/data/ailMel1/bed/tblastn.hg18KG/blastOut
for i in kg??
do
@@ -561,20 +560,19 @@
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: 83553 failed: 0 errors: 0
+# checked: 64037 failed: 0 errors: 0
# load table
ssh hgwdev
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
hgLoadPsl ailMel1 blastHg18KG.psl
# check coverage
featureBits ailMel1 blastHg18KG
-# 36312685 bases of 2231298548 (1.627%) in intersection
-
- featureBits ailMel1 blastHg18KG ensGene -enrichment
-# blastHg18KG 1.627%, ensGene 1.284%, both 0.845%, cover 51.91%, enrich 40.42x
+# 32308509 bases of 2245312831 (1.439%) in intersection
+ featureBits ailMel1 blastHg18KG xenoRefGene -enrichment
+# blastHg18KG 1.439%, xenoRefGene 2.186%, both 1.137%, cover 79.05%, enrich 36.17x
rm -rf blastOut
#end tblastn