src/hg/makeDb/doc/ce7.txt 1.2
1.2 2009/07/24 20:32:52 hiram
lastz runs done for caePb2, caeRem3, cb3, caeJap2
Index: src/hg/makeDb/doc/ce7.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ce7.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/doc/ce7.txt 23 Jul 2009 20:26:21 -0000 1.1
+++ src/hg/makeDb/doc/ce7.txt 24 Jul 2009 20:32:52 -0000 1.2
@@ -192,9 +192,9 @@
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF -verbose=2 -bigClusterHub=pk -workhorse=hgwdev \
-qRepeats=windowmaskerSdust -noLoadChainSplit -smallClusterHub=memk \
> do.log 2>&1 &
- # about 1h30m
+ # real 62m19.458s
# forgot the -qRepeats=windowmaskerSdust
rm axtChain/ce7.caePb2.net
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF -verbose=2 -bigClusterHub=pk -workhorse=hgwdev \
@@ -214,4 +214,154 @@
cat fb.caePb2.chainCe7Link.txt
# 55084634 bases of 170473138 (32.313%) in intersection
#########################################################################
+## BLASTZ caeJap2 (DONE - 2009-07-24 - Hiram)
+ screen # use screen to control the job
+ mkdir /hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24
+ cd /hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24
+
+ cat << '_EOF_' > DEF
+# ce7 vs caeJap2
+BLASTZ_H=2000
+BLASTZ_M=50
+
+# TARGET: elegans Ce7
+SEQ1_DIR=/scratch/data/ce7/ce7.2bit
+SEQ1_LEN=/scratch/data/ce7/chrom.sizes
+SEQ1_CHUNK=1000000
+SEQ1_LAP=10000
+
+# QUERY: C. japonica caeJap2
+SEQ2_DIR=/scratch/data/caeJap2/caeJap2.2bit
+SEQ2_LEN=/scratch/data/caeJap2/chrom.sizes
+SEQ2_CTGDIR=/scratch/data/caeJap2/caeJap2.supers.2bit
+SEQ2_CTGLEN=/scratch/data/caeJap2/caeJap2.supers.sizes
+SEQ2_LIFT=/scratch/data/caeJap2/caeJap2.chrUn.lift
+SEQ2_CHUNK=1000000
+SEQ2_LAP=0
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -bigClusterHub=pk -noLoadChainSplit -qRepeats=windowmaskerSdust \
+ -workhorse=hgwdev -smallClusterHub=memk > do.log 2>&1 &
+ # real 87m1.988s
+ cat fb.ce7.chainCaeJap2Link.txt
+ # 27270064 bases of 100286002 (27.192%) in intersection
+
+ # swap, this is also in caeJap2.txt
+ mkdir /hive/data/genomes/caeJap2/bed/blastz.ce7.swap
+ cd /hive/data/genomes/caeJap2/bed/blastz.ce7.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ -qRepeats=windowmaskerSdust -bigClusterHub=pk -noLoadChainSplit \
+ /hive/data/genomes/ce7/bed/lastzCaeJap2.2009-07-24/DEF \
+ -smallClusterHub=memk -swap > swap.log 2>&1 &
+ # real 4m23.124s
+ cat fb.caeJap2.chainCe7Link.txt
+ # 26441005 bases of 129295754 (20.450%) in intersection
+
+############################################################################
+## BLASTZ cb3 (DONE - 2009-07-24 - Hiram)
+ screen # use screen to control the job
+ mkdir /hive/data/genomes/ce7/bed/lastzCb3.2009-07-24
+ cd /hive/data/genomes/ce7/bed/lastzCb3.2009-07-24
+
+ cat << '_EOF_' > DEF
+# ce7 vs cb3
+BLASTZ_H=2000
+BLASTZ_M=50
+
+# TARGET: elegans Ce7
+SEQ1_DIR=/scratch/data/ce7/ce7.2bit
+SEQ1_LEN=/scratch/data/ce7/chrom.sizes
+SEQ1_CHUNK=1000000
+SEQ1_LAP=10000
+
+# QUERY: C. briggsae cb3
+SEQ2_DIR=/hive/data/genomes/cb3/cb3.rmskTrf.2bit
+SEQ2_LEN=/hive/data/genomes/cb3/chrom.sizes
+SEQ2_CHUNK=1000000
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/ce7/bed/lastzCb3.2009-07-24
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -workhorse=hgwdev -bigClusterHub=pk -noLoadChainSplit \
+ -smallClusterHub=memk > do.log 2>&1 &
+ # real 50m9.701s
+ cat fb.ce7.chainCb3Link.txt
+ # 42421335 bases of 100286002 (42.300%) in intersection
+
+ # swap, this is also in cb3.txt
+ mkdir /hive/data/genomes/cb3/bed/blastz.ce7.swap
+ cd /hive/data/genomes/cb3/bed/blastz.ce7.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/ce7/bed/lastzCb3.2009-07-24/DEF \
+ -workhorse=hgwdev -bigClusterHub=pk -noLoadChainSplit \
+ -smallClusterHub=memk -swap > swap.log 2>&1 &
+ # real 3m38.745s
+ cat fb.cb3.chainCe7Link.txt
+ # 43115929 bases of 108433446 (39.763%) in intersection
+
+############################################################################
+## BLASTZ caeRem3 (DONE - 2009-07-24,09 - Hiram)
+ screen # use screen to control the job
+ mkdir /hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24
+ cd /hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24
+
+ cat << '_EOF_' > DEF
+# ce7 vs caeRem3
+BLASTZ_H=2000
+BLASTZ_M=50
+
+# TARGET: elegans Ce7
+SEQ1_DIR=/scratch/data/ce7/ce7.2bit
+SEQ1_LEN=/scratch/data/ce7/chrom.sizes
+SEQ1_CHUNK=1000000
+SEQ1_LAP=10000
+
+# QUERY: C. remanei caeRem3
+SEQ2_DIR=/scratch/data/caeRem3/caeRem3.2bit
+SEQ2_LEN=/scratch/data/caeRem3/chrom.sizes
+SEQ2_CTGDIR=/scratch/data/caeRem3/caeRem3.supercontigs.2bit
+SEQ2_CTGLEN=/scratch/data/caeRem3/caeRem3.supercontigs.sizes
+SEQ2_LIFT=/scratch/data/caeRem3/caeRem3.chrUn.lift
+SEQ2_CHUNK=1000000
+SEQ2_LAP=0
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24
+TMPDIR=/scratch/tmp
+'_EOF_'
+ # << happy emacs
+
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ `pwd`/DEF \
+ -workhorse=hgwdev -bigClusterHub=swarm -noLoadChainSplit \
+ -qRepeats=windowmaskerSdust -smallClusterHub=memk > do.log 2>&1 &
+ # real 28m14.168s
+ cat fb.ce7.chainCaeRem3Link.txt
+ # 41841199 bases of 100286002 (41.722%) in intersection
+
+ # swap, this is also in caeRem3.txt
+ mkdir /hive/data/genomes/caeRem3/bed/blastz.ce7.swap
+ cd /hive/data/genomes/caeRem3/bed/blastz.ce7.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ -qRepeats=windowmaskerSdust \
+ -workhorse=hgwdev -noLoadChainSplit \
+ /hive/data/genomes/ce7/bed/lastzCaeRem3.2009-07-24/DEF \
+ -bigClusterHub=swarm -smallClusterHub=memk -swap > swap.log 2>&1 &
+ # real 2m53.936s
+ cat fb.caeRem3.chainCe7Link.txt
+ # 46320678 bases of 138406388 (33.467%) in intersection
+
+############################################################################