src/hg/makeDb/doc/hg19.txt 1.55

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.54
retrieving revision 1.55
diff -b -B -U 4 -r1.54 -r1.55
--- src/hg/makeDb/doc/hg19.txt	2 Nov 2009 18:24:53 -0000	1.54
+++ src/hg/makeDb/doc/hg19.txt	4 Nov 2009 04:17:05 -0000	1.55
@@ -7712,10 +7712,10 @@
 
     rm j*
 
 #########################################################################
-# hgPal downloads (working braney
-#   FASTA from 44way for refGene, knownGene, knownCanonical 
+# hgPal downloads (DONE braney 2009-11-03)
+#   FASTA from 46way for refGene, knownGene, knownCanonical 
 
     ssh hgwdev
     screen
     bash
@@ -7744,13 +7744,13 @@
     time sh -x $gp.jobs > $gp.jobs.log 2>&1 &
     sleep 1
     tail -f $gp.jobs.log
 
-# real    525m57.376s
-# user    25m36.072s
-# sys     7m41.565s
+# real    350m10.116s
+# user    38m38.731s
+# sys     7m22.106s
+
 
-    ssh kolossus
     mz=multiz46way
     gp=refGene
     db=hg19
     zcat exonAA/*.gz | gzip -c > $gp.$mz.exonAA.fa.gz
@@ -7789,11 +7789,9 @@
     time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1 &
     sleep 1
     tail -f $gp.$mz.job.log
 
-# real    442m46.735s
-# user    43m3.060s
-# sys     10m45.635s
+# oops... missed the timing
 
 
     mz=multiz46way
     gp=knownGene
@@ -7841,11 +7839,12 @@
     time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1 &
     sleep 1
     tail -f $gp.$mz.job.log
 
-# real    326m12.849s
-# user    17m40.850s
-# sys     3m59.648s
+# real    302m20.489s
+# user    27m31.179s
+# sys     5m30.071s
+
 
     rm *.known.bed
     mz=multiz46way
     gp=knownCanonical
@@ -7863,4 +7862,6 @@
     pd=/usr/local/apache/htdocs/goldenPath/$db/$mz/alignments
     mkdir -p $pd
     ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz
     ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz
+
+######################