src/hg/makeDb/doc/canFam2.txt 1.30

Index: src/hg/makeDb/doc/canFam2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/canFam2.txt,v
retrieving revision 1.29
retrieving revision 1.30
diff -b -B -U 4 -r1.29 -r1.30
--- src/hg/makeDb/doc/canFam2.txt	29 Mar 2010 22:12:22 -0000	1.29
+++ src/hg/makeDb/doc/canFam2.txt	30 Mar 2010 22:54:33 -0000	1.30
@@ -3085,45 +3085,11 @@
 	-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
     #	real    129m56.144s
     cat fb.calJac3.chainHg19Link.txt 
     #	1397333116 bases of 2752505800 (50.766%) in intersection
-#######################################################################
-# felCatV17e Cat BLASTZ/CHAIN/NET (working  - 2010-03-22 - Chin)
-    screen # use a screen to manage this multi-day job
-    mkdir /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
+#####################################################################
+# LASTZ Dog Swap (DONE - 2010-03-22 - Chin)
     cd /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
-
-    cat << '_EOF_' > DEF
-# dog vs. cat
-# maximum M allowed with lastz is only 254
-BLASTZ_M=254
-
-# TARGET: Dog canFan2
-SEQ1_DIR=/scratch/data/canFam2/canFam2.2bit
-SEQ1_LEN=/scratch/data/canFam2/chrom.sizes
-SEQ1_CHUNK=20000000
-SEQ1_LAP=10000
-SEQ1_LIMIT=5
-
-# QUERY: Cat (felCatV17e)
-SEQ2_DIR=/scratch/data/felCatV17e/felCatV17e.2bit
-SEQ2_LEN=/scratch/data/felCatV17e/chrom.sizes
-SEQ2_LIMIT=50
-SEQ2_CHUNK=10000000
-SEQ2_LAP=0
-
-BASE=/hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
-TMPDIR=/scratch/tmp
-'_EOF_'
-    # << this line keeps emacs coloring happy
-
-    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
-        `pwd`/DEF \
-        -syntenicNet -noDbNameCheck \
-        -chainMinScore=3000 -chainLinearGap=medium \
-        -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-        > do.log 2>&1 &
-    #   real    287m24.258s
     cat fb.canFam2.chainFelCatV17eLink.txt
     #  1481040604 bases of 2384996543 (62.098%) in intersection
 
     mkdir /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap
@@ -3134,9 +3100,10 @@
         -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
         -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
     #   real    251m14.341s
     # *** All done !  Elapsed time: 251m14s
-    # *** Make sure that goldenPath/felCatV17e/vsCanFam2/README.txt is accurate.
+    # *** Make sure that goldenPath/felCatV17e/vsCanFam2/README.txt is
+    # accurate.
     # *** Add {chain,net}CanFam2 tracks to trackDb.ra if necessary.
     cat fb.felCatV17e.chainCanFam2Link.txt
     # 1467506008 bases of 1990635005 (73.720%) in intersection