src/hg/makeDb/doc/felCatV17e.txt 1.4
1.4 2010/03/30 21:23:39 chinhli
Adding LASTZ Chain/Net support
Index: src/hg/makeDb/doc/felCatV17e.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/felCatV17e.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/makeDb/doc/felCatV17e.txt 22 Mar 2010 16:55:46 -0000 1.3
+++ src/hg/makeDb/doc/felCatV17e.txt 30 Mar 2010 21:23:39 -0000 1.4
@@ -441,9 +441,8 @@
# Average job time: 9s 0.15m 0.00h 0.00d
# Longest finished job: 174s 2.90m 0.05h 0.00d
# Submission to last job: 1136s 18.93m 0.32h 0.01d
-XXXX
# Transform cpglh output to bed +
catDir results | awk '{
$2 = $2 - 1;
width = $3 - $2;
@@ -461,12 +460,118 @@
# Creating table definition for cpgIslandExt
# Saving bed.tab
# Loading felCatV17e
- # check iy with featureBits felCatV17e cpgIslandExt
+ # check it with featureBits felCatV17e cpgIslandExt
# 36646772 bases of 1990635005 (1.841%) in intersection
# cleanup
rm -fr hardMaskedFa
+#####################################################################
+# LASTZ Dog Swap (DONE - 2010-03-22 - Chin)
+ cd /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
+ cat fb.canFam2.chainFelCatV17eLink.txt
+ # 1481040604 bases of 2384996543 (62.098%) in intersection
+
+ mkdir /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap
+ cd /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22/DEF \
+ -swap -syntenicNet -noDbNameCheck \
+ -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.
+ # *** Add {chain,net}CanFam2 tracks to trackDb.ra if necessary.
+ cat fb.felCatV17e.chainCanFam2Link.txt
+ # 1467506008 bases of 1990635005 (73.720%) in intersection
+
+#####################################################################
+# LASTZ Mouse Swap (DONE - 2010-03-22 - Chin)
+ cd /hive/data/genomes/mm9/bed/lastzFelCatV17e.2010-03-22
+ cat fb.mm9.chainFelCatV17eLink.txt
+ # 637007193 bases of 2620346127 (24.310%) in intersection
+ # swap
+ mkdir /hive/data/genomes/felCatV17e/bed/blastz.mm9.swap
+ cd /hive/data/genomes/felCatV17e/bed/blastz.mm9.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/mm9/bed/lastzFelCatV17e.2010-03-22/DEF \
+ -swap -syntenicNet -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 125m37.926s
+ cat fb.felCatV17e.chainMm9Link.txt
+ # 616529959 bases of 1990635005 (30.972%) in intersection
+
+
+#####################################################################
+# LASTZ Human Swap (DONE - 2010-03-22 - Chin)
+ cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
+ cat fb.hg19.chainFelCatV17eLink.txt
+ # 1266003011 bases of 2897316137 (43.696%) in intersection
+
+ # Swap
+ mkdir /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
+ cd /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22/DEF \
+ -swap -syntenicNet -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=pk \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 120m42.991s
+ cat fb.felCatV17e.chainHg19Link.txt
+ # 2030475813 bases of 2752505800 (73.768%) in intersection
+
+
+#####################################################################
+# LASTZ Panda Swap (DONE - 2010-03-22 - Chin)
+ cd /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22
+ cat fb.felCatV17e.chainAilMel1Link.txt
+ # 1503647735 bases of 1990635005 (75.536%) in intersection
+
+ mkdir /hive/data/genomes/felCatV17e/bed/blastz.ailMel1.swap
+ cd /hive/data/genomes/felCatV17e/bed/blastz.ailMel1.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22/DEF \
+ -swap -syntenicNet -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
+ # real 155m57.566s
+ cat fb.ailMel1.chainFelCatV17eLink.txt
+ # 1507273252 bases of 2245312831 (67.130%) in intersection
+
+
+
+
+#####################################################################
+# LASTZ Oppsom Swap (DONE - 2010-03-22 - Chin)
+ cd /hive/data/genomes/monDom5/bed/lastzFelCatV17e.2010-03-22
+ cat fb.monDom5.chainFelCatV17eLink.txt
+ # 178616721 bases of 3501660299 (5.101%) in intersection
+
+ # Swap
+ mkdir /hive/data/genomes/felCatV17e/bed/blastz.monDom5.swap
+ cd /hive/data/genomes/felCatV17e/bed/blastz.monDom5.swap
+ time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/monDom5/bed/lastzFelCatV17e.2010-03-22/DEF \
+ -swap -syntenicNet -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
+ -chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
+ # *** All done ! Elapsed time: 100m29s
+ # *** Make sure that goldenPath/felCatV17e/vsMonDom5/README.txt is
+ # accurate.
+ # *** Add {chain,net}MonDom5 tracks to trackDb.ra if necessary.
+
+ cat fb.felCatV17e.chainMonDom5Link.txt
+ # 166499264 bases of 1990635005 (8.364%) in intersection
+
+
+
+
+
+####################################################################
+