#########################################################################
# crispr whole genome (WORKING - 2019-07-03 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/crisprAll
    cd /hive/data/genomes/hg38/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 \
    hg38 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev-101 -bigClusterHub=ku \
      -workhorse=hgwdev) > ranges.log 2>&1
    # real    3m27.509s


    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=guides -stop=guides \
    hg38 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > guides.log 2>&1
    # real    13m30.089s

    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=specScoreJobList -stop=specScores \
    hg38 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > specScores.log 2>&1
# 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 \
    hg38 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > load.log 2>&1
    # real    1085m38.773s

    # cleaning up 2021-04-24 - Hiram
    time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \
       -continue=cleanup \
    hg38 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev) > cleanup.log 2>&1

#########################################################################

