2a038de3ff8f6ef5242536a5f5e94fcc0c65f652
hiram
  Tue Oct 8 15:56:13 2019 -0700
running up crisprAll track for mm10 no redmine

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index b31d057..ff63212 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18192,15 +18192,56 @@
 	-chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
     #	real    94m19.060s
 
     cat fb.regenRn1.chainMm10Link.txt
     #   1634389849 bases of 2282482188 (71.606%) in intersection
     cat fb.regenRn1.chainSynMm10Link.txt
     #   1564752158 bases of 2282482188 (68.555%) in intersection
 
     time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 mm10) > rbest.log 2>&1
     # real    488m25.471s
 
     cat fb.regenRn1.chainRBest.Mm10.txt
     # 1565313924 bases of 2282482188 (68.579%) in intersection
 
 ##############################################################################
+# crispr whole genome (WORKING - 2019-10-08 - Hiram)
+    mkdir /hive/data/genomes/mm10/bed/crisprAll
+    cd /hive/data/genomes/mm10/bed/crisprAll
+
+    # the large shoulder argument will cause the entire genome to be scanned
+    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \
+    mm10 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
+    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
+      -workhorse=hgwdev) > ranges.log 2>&1
+    # real    2m58.652s
+
+    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
+       -continue=guides -stop=guides \
+    mm10 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
+    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
+      -workhorse=hgwdev) > guides.log 2>&1
+    # real    8m40.172s
+
+    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
+       -continue=specScoreJobList -stop=specScores \
+    mm10 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
+    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
+      -workhorse=hgwdev) > specScores.log 2>&1
+XXX - running - Tue Oct  8 15:49:19 PDT 2019
+# Completed: 3147278 of 3147278 jobs
+# CPU time in finished jobs:  301358514s 5022641.91m 83710.70h 3487.95d  9.556 y
+# IO & Wait Time:             153270388s 2554506.46m 42575.11h 1773.96d  4.860 y
+# Average job time:                 144s       2.41m     0.04h    0.00d
+# Longest finished job:             388s       6.47m     0.11h    0.00d
+# Submission to last job:        458446s    7640.77m   127.35h    5.31d
+
+    ### remember to get back to hgwdev to run this
+    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
+       -continue=effScores -stop=load \
+    mm10 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
+    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
+      -workhorse=hgwdev) > load.log 2>&1
+    # real    1085m38.773s
+
+#########################################################################
+