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 + +######################################################################### +