#############################################################################
## 30-Way Multiz (DONE - 2017-10-19 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/hg38/bed/multiz30way
    cd /hive/data/genomes/hg38/bed/multiz30way

    # from the 218-way in the source tree, select out the 30 used here:
    /cluster/bin/phast/tree_doctor \
        --prune-all-but aotNan1,calJac3,cebCap1,cerAty1,chlSab2,colAng1,eulFla1,eulMac1,gorGor5,hg38,macFas5,macNem1,manLeu1,micMur3,nasLar1,nomLeu3,otoGar3,panPan2,panTro5,papAnu3,ponAbe2,proCoq1,rheMac8,rhiBie1,rhiRox1,saiBol1,tarSyr2,canFam3,dasNov3,mm10 \
        /cluster/home/hiram/kent/src/hg/utils/phyloTrees/218way.nh \
          > t.nh

    # using TreeGraph2 tree editor on the Mac, rearrange to get hg38
    # at the top, and attempt to get the others in phylo order:
    /cluster/bin/phast/all_dists t.nh | grep hg38 \
        | sed -e "s/hg38.//" | sort -k2n | sed -e 's/^/#\t/;'
#       panTro5 0.013390
#       panPan2 0.015610
#       gorGor5 0.019734
#       ponAbe2 0.039403
#       nomLeu3 0.046204
#       nasLar1 0.075474
#       rhiBie1 0.075474
#       rhiRox1 0.075474
#       colAng1 0.075574
#       macFas5 0.079575
#       rheMac8 0.079575
#       papAnu3 0.079626
#       macNem1 0.081584
#       cerAty1 0.082584
#       saiBol1 0.087804
#       chlSab2 0.087974
#       manLeu1 0.090974
#       aotNan1 0.102804
#       calJac3 0.107454
#       cebCap1 0.108804
#       eulFla1 0.190934
#       eulMac1 0.190934
#       tarSyr2 0.221294
#       proCoq1 0.230934
#       micMur3 0.236534
#       otoGar3 0.270334
#       canFam3 0.332429
#       dasNov3 0.366691
#       mm10    0.502391

    #	what that looks like:
~/kent/src/hg/utils/phyloTrees/asciiTree.pl t.nh > hg38.30way.nh
~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.30way.nh | sed -e 's/^/# /;'

# ((((((((((((hg38:0.00655,
#            panTro5:0.00684):0.00122,
#           panPan2:0.00784):0.003,
#          gorGor5:0.008964):0.009693,
#         ponAbe2:0.01894):0.003471,
#        nomLeu3:0.02227):0.01204,
#       (((((rheMac8:0.003991,
#           (macFas5:0.002991,
#           macNem1:0.005000):0.001000):0.001000,
#          cerAty1:0.008):0.005,
#         papAnu3:0.010042):0.01061,
#        (chlSab2:0.027,
#        manLeu1:0.030000):0.002000):0.003000,
#       ((nasLar1:0.0007,
#        colAng1:0.0008):0.0008,
#       (rhiRox1:0.0007,
#       rhiBie1:0.000700):0.000800):0.018000):0.020000):0.021830,
#      (((calJac3:0.03,
#        saiBol1:0.01035):0.00865,
#       cebCap1:0.04):0.006,
#      aotNan1:0.040000):0.005000):0.052090,
#     tarSyr2:0.1114):0.02052,
#    (((micMur3:0.0556,
#      proCoq1:0.05):0.015,
#     (eulMac1:0.01,
#     eulFla1:0.010000):0.015000):0.015000,
#    otoGar3:0.119400):0.020520):0.015494,
#   mm10:0.356483):0.020593,
#  canFam3:0.165928):0.023664,
# dasNov3:0.176526);

    # extract species list from that .nh file
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        hg38.30way.nh | xargs echo | sed 's/ //g; s/,/ /g' \
        | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt

    # construct db to name translation list:
    cat species.list.txt | while read DB
do
hgsql -N -e "select name,organism from dbDb where name=\"${DB}\";" hgcentraltest
done | sed -e "s/\t/->/; s/ /_/g;" | sed -e 's/$/;/' | sed -e 's/\./_/g' \
    | sed -e "s#'#_x_#g;" > db.to.name.txt

# edited db.to.name.txt to change - to _ in some of the names.
# e.g. Crab-eating -> Crab_eating,
# the Crab-eating didn't survive the tree_doctor

/cluster/bin/phast/tree_doctor --rename "`cat db.to.name.txt`" hg38.30way.nh \
   | sed -e 's/0\+)/)/g; s/0\+,/,/g' \
     | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
       | sed -e "s#_x_#'#g;" > hg38.30way.commonNames.nh

    cat hg38.30way.commonNames.nh | sed -e 's/^/# /;'
# ((((((((((((Human:0.00655,
#            Chimp:0.00684):0.00122,
#           Bonobo:0.00784):0.003,
#          Gorilla:0.008964):0.009693,
#         Orangutan:0.01894):0.003471,
#        Gibbon:0.02227):0.01204,
#       (((((Rhesus:0.003991,
#           (Crab_eating_macaque:0.002991,
#           Pig_tailed_macaque:0.005):0.001):0.001,
#          Sooty_mangabey:0.008):0.005,
#         Baboon:0.010042):0.01061,
#        (Green_monkey:0.027,
#        Drill:0.03):0.002):0.003,
#       ((Proboscis_monkey:0.0007,
#        Angolan_colobus:0.0008):0.0008,
#       (Golden_snub:0.0007,
#       Black_snub:0.0007):0.0008):0.018):0.02):0.02183,
#      (((Marmoset:0.03,
#        Squirrel_monkey:0.01035):0.00865,
#       White_faced_sapajou:0.04):0.006,
#      Ma's_night_monkey:0.04):0.005):0.05209,
#     Tarsier:0.1114):0.02052,
#    (((Mouse_lemur:0.0556,
#      Coquerel's_sifaka:0.05):0.015,
#     (Black_lemur:0.01,
#     Sclater's_lemur:0.01):0.015):0.015,
#    Bushbaby:0.1194):0.02052):0.015494,
#   Mouse:0.356483):0.020593,
#  Dog:0.165928):0.023664,
# Armadillo:0.176526);

#	Use this specification in the phyloGif tool:
#	http://genome.ucsc.edu/cgi-bin/phyloGif
#	to obtain a png image for src/hg/htdocs/images/phylo/hg38_30way.png

    ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.30way.nh > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
          > hg38.30way.scientificNames.nh
    rm -f t.nh
    cat hg38.30way.scientificNames.nh | sed -e 's/^/# /;'
# ((((((((((((Homo_sapiens:0.00655,
#            Pan_troglodytes:0.00684):0.00122,
#           Pan_paniscus:0.00784):0.003,
#          Gorilla_gorilla_gorilla:0.008964):0.009693,
#         Pongo_pygmaeus_abelii:0.01894):0.003471,
#        Nomascus_leucogenys:0.02227):0.01204,
#       (((((Macaca_mulatta:0.003991,
#           (Macaca_fascicularis:0.002991,
#           Macaca_nemestrina:0.005):0.001):0.001,
#          Cercocebus_atys:0.008):0.005,
#         Papio_anubis:0.010042):0.01061,
#        (Chlorocebus_sabaeus:0.027,
#        Mandrillus_leucophaeus:0.03):0.002):0.003,
#       ((Nasalis_larvatus:0.0007,
#        Colobus_angolensis_palliatus:0.0008):0.0008,
#       (Rhinopithecus_roxellana:0.0007,
#       Rhinopithecus_bieti:0.0007):0.0008):0.018):0.02):0.02183,
#      (((Callithrix_jacchus:0.03,
#        Saimiri_boliviensis:0.01035):0.00865,
#       Cebus_capucinus_imitator:0.04):0.006,
#      Aotus_nancymaae:0.04):0.005):0.05209,
#     Tarsius_syrichta:0.1114):0.02052,
#    (((Microcebus_murinus:0.0556,
#      Propithecus_coquereli:0.05):0.015,
#     (Eulemur_macaco:0.01,
#     Eulemur_flavifrons:0.01):0.015):0.015,
#    Otolemur_garnettii:0.1194):0.02052):0.015494,
#   Mus_musculus:0.356483):0.020593,
#  Canis_lupus_familiaris:0.165928):0.023664,
# Dasypus_novemcinctus:0.176526);

    /cluster/bin/phast/all_dists hg38.30way.nh | grep hg38 \
        | sed -e "s/hg38.//" | sort -k2n > 30way.distances.txt
    #	Use this output to create the table below
    cat 30way.distances.txt | sed -e 's/^/# /;'
# panTro5       0.013390
# panPan2       0.015610
# gorGor5       0.019734
# ponAbe2       0.039403
# nomLeu3       0.046204
# nasLar1       0.075474
# rhiBie1       0.075474
# rhiRox1       0.075474
# colAng1       0.075574
# macFas5       0.079575
# rheMac8       0.079575
# papAnu3       0.079626
# macNem1       0.081584
# cerAty1       0.082584
# saiBol1       0.087804
# chlSab2       0.087974
# manLeu1       0.090974
# aotNan1       0.102804
# calJac3       0.107454
# cebCap1       0.108804
# eulFla1       0.190934
# eulMac1       0.190934
# tarSyr2       0.221294
# proCoq1       0.230934
# micMur3       0.236534
# otoGar3       0.270334
# canFam3       0.332429
# dasNov3       0.366691
# mm10  0.502391

    printf '#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<30way.distances.txt") or
        die "can not read 30way.distances.txt";

my $count = 0;
while (my $line = <FH>) {
    chomp $line;
    my ($D, $dist) = split('"'"'\\s+'"'"', $line);
    my $chain = "chain" . ucfirst($D);
    my $B="/hive/data/genomes/hg38/bed/lastz.$D/fb.hg38." .
        $chain . "Link.txt";
    my $chainLinkMeasure =
        `awk '"'"'{print \\$5}'"'"' ${B} 2> /dev/null | sed -e "s/(//; s/)//"`;
    chomp $chainLinkMeasure;
    $chainLinkMeasure = 0.0 if (length($chainLinkMeasure) < 1);
    $chainLinkMeasure =~ s/\\%%//;
    my $swapFile="/hive/data/genomes/${D}/bed/lastz.hg38/fb.${D}.chainHg38Link.txt";
    my $swapMeasure = "N/A";
    if ( -s $swapFile ) {
	$swapMeasure =
	    `awk '"'"'{print \\$5}'"'"' ${swapFile} 2> /dev/null | sed -e "s/(//; s/)//"`;
	chomp $swapMeasure;
	$swapMeasure = 0.0 if (length($swapMeasure) < 1);
	$swapMeasure =~ s/\\%%//;
    }
    my $orgName=
    `hgsql -N -e "select organism from dbDb where name='"'"'$D'"'"';" hgcentraltest`;
    chomp $orgName;
    if (length($orgName) < 1) {
        $orgName="N/A";
    }
    ++$count;
    printf "# %%02d  %%.4f (%%%% %%06.3f) (%%%% %%06.3f) - %%s %%s\\n", $count, $dist,
        $chainLinkMeasure, $swapMeasure, $orgName, $D;
}
close (FH);
' > sizeStats.pl
    chmod +x ./sizeStats.pl
    ./sizeStats.pl

#	If you can fill in all the numbers in this table, you are ready for
#	the multiple alignment procedure

#       featureBits chainLink measures
#               chainLink
#  N distance  on hg38  on other     other species
# 01  0.0134 (% 95.355) (% 93.714) - Chimp panTro5
# 02  0.0156 (% 92.685) (% 97.742) - Bonobo panPan2
# 03  0.0197 (% 94.691) (% 89.804) - Gorilla gorGor5
# 04  0.0394 (% 89.187) (% 89.656) - Orangutan ponAbe2
# 05  0.0462 (% 86.379) (% 90.470) - Gibbon nomLeu3
# 06  0.0755 (% 74.541) (% 89.972) - Proboscis monkey nasLar1
# 07  0.0755 (% 83.065) (% 81.306) - Black snub-nosed monkey rhiBie1
# 08  0.0755 (% 85.109) (% 86.629) - Golden snub-nosed monkey rhiRox1
# 09  0.0756 (% 81.641) (% 87.875) - Angolan colobus colAng1
# 10  0.0796 (% 85.675) (% 87.749) - Crab-eating macaque macFas5
# 11  0.0796 (% 84.506) (% 79.540) - Rhesus rheMac8
# 12  0.0796 (% 86.336) (% 86.461) - Baboon papAnu3
# 13  0.0816 (% 83.524) (% 85.402) - Pig-tailed macaque macNem1
# 14  0.0826 (% 83.847) (% 86.974) - Sooty mangabey cerAty1
# 15  0.0878 (% 70.565) (% 81.466) - Squirrel monkey saiBol1
# 16  0.0880 (% 84.393) (% 88.264) - Green monkey chlSab2
# 17  0.0910 (% 82.498) (% 88.550) - Drill manLeu1
# 18  0.1028 (% 70.629) (% 77.791) - Ma's night monkey aotNan1
# 19  0.1075 (% 71.709) (% 76.757) - Marmoset calJac3
# 20  0.1088 (% 70.683) (% 78.656) - White-faced sapajou cebCap1
# 21  0.1909 (% 33.326) (% 46.309) - Sclater's lemur eulFla1
# 22  0.1909 (% 33.708) (% 46.640) - Black lemur eulMac1
# 23  0.2213 (% 56.022) (% 52.305) - Tarsier tarSyr2
# 24  0.2309 (% 32.467) (% 45.739) - Coquerel's sifaka proCoq1
# 25  0.2365 (% 29.728) (% 36.904) - Mouse lemur micMur3
# 26  0.2703 (% 53.196) (% 64.899) - Bushbaby otoGar3
# 27  0.3324 (% 50.395) (% 60.861) - Dog canFam3
# 28  0.3667 (% 45.349) (% 41.895) - Armadillo dasNov3
# 29  0.5024 (% 31.653) (% 35.372) - Mouse mm10

# None of this concern for distances matters in building the first step, the
# maf files.  The distances will be better calibrated later.

    # create species list and stripped down tree for autoMZ
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	hg38.30way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh

    sed 's/[()]//g; s/,/ /g' tree.nh > species.list
    cat species.list | fold -s -w 76 | sed -e 's/^/# /;'
# hg38 panTro5 panPan2 gorGor5 ponAbe2 nomLeu3 rheMac8 macFas5 macNem1
# cerAty1 papAnu3 chlSab2 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 calJac3
# saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1 otoGar3
# mm10 canFam3 dasNov3

    #	bash shell syntax here ...
    cd /hive/data/genomes/hg38/bed/multiz30way
    export H=/hive/data/genomes/hg38/bed
    mkdir mafLinks
    # good, phylo close  assemblies can use syntenic net:
    for G in panTro5 panPan2 gorGor5 nomLeu3 colAng1 macFas5 rheMac8 macNem1 \
cerAty1 saiBol1 chlSab2 manLeu1 aotNan1 calJac3 cebCap1 proCoq1 micMur3 \
otoGar3 canFam3 dasNov3 mm10
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/axtChain/hg38.${G}.synNet.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/axtChain/hg38.${G}.synNet.maf.gz ./mafLinks/$G
    done

    # other assemblies using recip best net:
    #
    for G in ponAbe2 nasLar1 rhiBie1 rhiRox1 papAnu3 eulFla1 eulMac1 tarSyr2
    do
      mkdir mafLinks/$G
      echo ln -s ${H}/lastz.$G/mafRBestNet/hg38.${G}.rbest.maf.gz ./mafLinks/$G
      ln -s ${H}/lastz.$G/mafRBestNet/hg38.${G}.rbest.maf.gz ./mafLinks/$G
    done

    # verify the symLinks are good:
    ls -ogL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;'
#  1234251218 Sep 25 17:10 mafLinks/aotNan1/hg38.aotNan1.synNet.maf.gz
#  1275300135 Dec 13  2014 mafLinks/calJac3/hg38.calJac3.synNet.maf.gz
#  1098577678 Apr 10  2015 mafLinks/canFam3/hg38.canFam3.synNet.maf.gz
#  1254406823 Sep 28 20:27 mafLinks/cebCap1/hg38.cebCap1.synNet.maf.gz
#  1364636284 Sep 27 12:27 mafLinks/cerAty1/hg38.cerAty1.synNet.maf.gz
#  1375738965 Jul 11  2014 mafLinks/chlSab2/hg38.chlSab2.synNet.maf.gz
#  1317115105 Feb 27  2017 mafLinks/colAng1/hg38.colAng1.synNet.maf.gz
#   973195648 Apr 29  2015 mafLinks/dasNov3/hg38.dasNov3.synNet.maf.gz
#   669135484 Oct  5 14:41 mafLinks/eulFla1/hg38.eulFla1.rbest.maf.gz
#   677123602 Oct  5 13:04 mafLinks/eulMac1/hg38.eulMac1.rbest.maf.gz
#  1649008320 Jun 25  2016 mafLinks/gorGor5/hg38.gorGor5.synNet.maf.gz
#  1403994424 Dec 14  2014 mafLinks/macFas5/hg38.macFas5.synNet.maf.gz
#  1356256046 Feb 27  2017 mafLinks/macNem1/hg38.macNem1.synNet.maf.gz
#  1334057905 Sep 25 10:05 mafLinks/manLeu1/hg38.manLeu1.synNet.maf.gz
#   611966540 Mar  4  2017 mafLinks/micMur3/hg38.micMur3.synNet.maf.gz
#   710111073 Apr  9  2015 mafLinks/mm10/hg38.mm10.synNet.maf.gz
#  1145326563 Dec 15  2014 mafLinks/nasLar1/hg38.nasLar1.rbest.maf.gz
#  1333531476 Dec 12  2014 mafLinks/nomLeu3/hg38.nomLeu3.synNet.maf.gz
#  1130201295 Feb 23  2015 mafLinks/otoGar3/hg38.otoGar3.synNet.maf.gz
#  1514679150 May 24  2016 mafLinks/panPan2/hg38.panPan2.synNet.maf.gz
#  1642086478 Aug  4  2016 mafLinks/panTro5/hg38.panTro5.synNet.maf.gz
#  1336353318 Jun 22 23:34 mafLinks/papAnu3/hg38.papAnu3.rbest.maf.gz
#  1274517712 Sep  3  2014 mafLinks/ponAbe2/hg38.ponAbe2.rbest.maf.gz
#   652745807 Sep 28 19:12 mafLinks/proCoq1/hg38.proCoq1.synNet.maf.gz
#  1369672577 Feb  8  2016 mafLinks/rheMac8/hg38.rheMac8.synNet.maf.gz
#  1268717561 Mar 29  2017 mafLinks/rhiBie1/hg38.rhiBie1.rbest.maf.gz
#  1312210382 Feb 24  2015 mafLinks/rhiRox1/hg38.rhiRox1.rbest.maf.gz
#  1257517046 Dec 13  2014 mafLinks/saiBol1/hg38.saiBol1.synNet.maf.gz
#  1109719031 Dec 13  2014 mafLinks/tarSyr2/hg38.tarSyr2.rbest.maf.gz

    #	need to split these things up into smaller pieces for
    #	efficient kluster run.
    mkdir /hive/data/genomes/hg38/bed/multiz30way/mafSplit
    cd /hive/data/genomes/hg38/bed/multiz30way/mafSplit

    #	mafSplitPos splits on gaps or repeat areas that will not have
    #	any chains, approx 5 Mbp intervals, gaps at least 10,000
    mafSplitPos -minGap=10000 hg38 5 stdout | sort -u \
	| sort -k1,1 -k2,2n > mafSplit.bed
    #   see also multiz30way.txt for more discussion of this procedure

    #	run a kluster job to split them all
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz30way/mafSplit

    printf '
#!/bin/csh -ef
set G = $1
set M = $2
mkdir -p $G
pushd $G > /dev/null
if ( -s hg38_${M}.00.maf ) then
    /bin/rm -f hg38_${M}.*.maf
endif
/cluster/bin/x86_64/mafSplit ../mafSplit.bed hg38_ ../../mafLinks/${G}/${M}.maf.gz
/bin/gzip hg38_*.maf
popd > /dev/null
' > runOne

    # << happy emacs
    chmod +x runOne

    printf '#LOOP
runOne $(dir1) $(file1) {check out exists+ $(dir1)/hg38_chr1.00.maf.gz}
#ENDLOOP
' > template

    find ../mafLinks -type l | awk -F'/' '{printf "%s/%s\n", $3,$4}' \
      | sed -e 's/.maf.gz//;' > maf.list

    gensub2 maf.list single template jobList
    para -ram=16g create jobList
    para try ... check ... push ... etc...
# Completed: 29 of 29 jobs
# CPU time in finished jobs:      31855s     530.92m     8.85h    0.37d  0.001 y
# IO & Wait Time:                     0s       0.00m     0.00h    0.00d  0.000 y
# Average job time:                1070s      17.84m     0.30h    0.01d
# Longest finished job:            1544s      25.73m     0.43h    0.02d
# Submission to last job:          3302s      55.03m     0.92h    0.04d

    # construct a list of all possible maf file names.
    # they do not all exist in each of the species directories
    find . -type f | grep "maf.gz" | wc -l
    # 16567

    find . -type f | grep ".maf.gz$" | xargs -L 1 basename | sort -u \
        > run.maf.list
    wc -l run.maf.list
    # 678 run.maf.list

    # number of chroms with data:
    awk -F'.' '{print $1}' run.maf.list  | sed -e 's/hg38_//;' \
      | sort | uniq -c | sort -n | wc -l
    #  358

    mkdir /hive/data/genomes/hg38/bed/multiz30way/splitRun
    cd /hive/data/genomes/hg38/bed/multiz30way/splitRun
    mkdir maf run
    cd run
    mkdir penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/multiz penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/maf_project penn
    cp -p /cluster/bin/penn/multiz.2009-01-21_patched/autoMZ penn

    #	set the db and pairs directories here
    cat > autoMultiz.csh << '_EOF_'
#!/bin/csh -ef
set db = hg38
set c = $1
set result = $2
set run = `/bin/pwd`
set tmp = /dev/shm/$db/multiz.$c
set pairs = /hive/data/genomes/hg38/bed/multiz30way/mafSplit
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
/bin/cp -p ../../tree.nh ../../species.list $tmp
pushd $tmp > /dev/null
foreach s (`/bin/sed -e "s/$db //" species.list`)
    set in = $pairs/$s/$c
    set out = $db.$s.sing.maf
    if (-e $in.gz) then
        /bin/zcat $in.gz > $out
        if (! -s $out) then
            echo "##maf version=1 scoring=autoMZ" > $out
        endif
    else if (-e $in) then
        /bin/ln -s $in $out
    else
        echo "##maf version=1 scoring=autoMZ" > $out
    endif
end
set path = ($run/penn $path); rehash
$run/penn/autoMZ + T=$tmp E=$db "`cat tree.nh`" $db.*.sing.maf $c \
        > /dev/null
popd > /dev/null
/bin/rm -f $result
/bin/cp -p $tmp/$c $result
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty /dev/shm/$db
'_EOF_'
# << happy emacs
    chmod +x autoMultiz.csh

    printf '#LOOP
./autoMultiz.csh $(root1) {check out line+ /hive/data/genomes/hg38/bed/multiz30way/splitRun/maf/$(root1)}
#ENDLOOP
' > template

    ln -s  ../../mafSplit/run.maf.list maf.list

    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz30way/splitRun/run
    gensub2 maf.list single template jobList
    para create jobList
    para try ... check ... push ... etc...
# Completed: 678 of 678 jobs
# CPU time in finished jobs:    3849518s   64158.63m  1069.31h   44.55d  0.122 y
# IO & Wait Time:                  4040s      67.33m     1.12h    0.05d  0.000 y
# Average job time:                5684s      94.73m     1.58h    0.07d
# Longest finished job:           37569s     626.15m    10.44h    0.43d
# Submission to last job:         79158s    1319.30m    21.99h    0.92d

    # put the split maf results back together into a single per-chrom maf file
    #	eliminate duplicate comments
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/splitRun
    mkdir ../maf
    #	no need to save the comments since they are lost with mafAddIRows

    cat << '_EOF_' >> runOne
#!/bin/csh -fe
set C = $1
if ( -s ../maf/${C}.maf.gz ) then
    rm -f ../maf/${C}.maf.gz
endif
if ( -s maf/hg38_${C}.00.maf ) then
  head -q -n 1 maf/hg38_${C}.00.maf | sort -u > ../maf/${C}.maf
  grep -h -v "^#" `ls maf/hg38_${C}.*.maf | sort -t. -k2,2n` >> ../maf/${C}.maf
  tail -q -n 1 maf/hg38_${C}.00.maf | sort -u >> ../maf/${C}.maf
else
  touch ../maf/${C}.maf
endif
'_EOF_'
    # << happy emacs
    chmod +x runOne

    cat << '_EOF_' >> template
#LOOP
runOne $(root1) {check out exists ../maf/$(root1).maf}
#ENDLOOP
'_EOF_'
    # << happy emacs

    cut -f1 ../../../chrom.sizes > chr.list
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz30way/splitRun
    gensub2 chr.list single template jobList
    para -ram=16g create jobList
    para try ... check ... push ... etc ...
    para -maxJob=32 push
# Completed: 455 of 455 jobs
# CPU time in finished jobs:        265s       4.42m     0.07h    0.00d  0.000 y
# IO & Wait Time:                  1472s      24.53m     0.41h    0.02d  0.000 y
# Average job time:                   4s       0.06m     0.00h    0.00d
# Longest finished job:              52s       0.87m     0.01h    0.00d
# Submission to last job:            92s       1.53m     0.03h    0.00d

    cd /hive/data/genomes/hg38/bed/multiz30way/maf
    # 97 of them have empty results, they have to be removed
    ls -ogrt | awk '$3 == 0' | awk '{print $NF}' | xargs rm -f


    # Load into database
    mkdir -p /gbdb/hg38/multiz30way/maf
    cd /hive/data/genomes/hg38/bed/multiz30way/maf
    ln -s `pwd`/*.maf /gbdb/hg38/multiz30way/maf/

    # this generates an immense multiz30way.tab file in the directory
    #	where it is running.  Best to run this over in scratch.
    #   This is going to take all day.
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/hg38/multiz30way/maf hg38 multiz30way
    # Loaded 40625470 mafs in 358 files from /gbdb/hg38/multiz30way/maf
    # real    28m23.045s

    time (cat /gbdb/hg38/multiz30way/maf/*.maf \
        | hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 hg38 multiz30waySummary stdin)
#  Created 4568973 summary blocks from 850984320 components and 40625470 mafs from stdin
#  real    49m52.561s


-rw-rw-r--   1 2171190193 Nov  2 16:40 multiz30way.tab
-rw-rw-r--   1  215756735 Nov  2 17:44 multiz30waySummary.tab

    wc -l multiz30*.tab
#    40625470 multiz30way.tab
#     4568973 multiz30waySummary.tab

    rm multiz30way*.tab

#######################################################################
# GAP ANNOTATE MULTIZ30WAY MAF AND LOAD TABLES (DONE - 2017-11-03 - Hiram)
    # mafAddIRows has to be run on single chromosome maf files, it does not
    #	function correctly when more than one reference sequence
    #	are in a single file.
    mkdir -p /hive/data/genomes/hg38/bed/multiz30way/anno
    cd /hive/data/genomes/hg38/bed/multiz30way/anno

    # check for N.bed files everywhere:
    for DB in `cat ../species.list`
do
    if [ ! -s /hive/data/genomes/${DB}/${DB}.N.bed ]; then
        echo "MISS: ${DB}"
        cd /hive/data/genomes/${DB}
        twoBitInfo -nBed ${DB}.2bit ${DB}.N.bed
    else
        echo "  OK: ${DB}"
    fi
    cd /hive/data/genomes/hg38/bed/multiz30way/anno
done

    cd /hive/data/genomes/hg38/bed/multiz30way/anno
    for DB in `cat ../species.list`
do
    echo "${DB} "
    ln -s  /hive/data/genomes/${DB}/${DB}.N.bed ${DB}.bed
    echo ${DB}.bed  >> nBeds
    ln -s  /hive/data/genomes/${DB}/chrom.sizes ${DB}.len
    echo ${DB}.len  >> sizes
done
    # make sure they all are successful symLinks:
    ls -ogrtL *.bed | wc -l
    # 30

    screen -S hg38      # use a screen to control this longish job
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz30way/anno
    mkdir result

    cat << '_EOF_' > template
#LOOP
mafAddIRows -nBeds=nBeds $(path1) /hive/data/genomes/hg38/hg38.2bit {check out line+ result/$(file1)}
#ENDLOOP
'_EOF_'
    # << happy emacs

    ls ../maf/*.maf > maf.list
    gensub2 maf.list single template jobList
    # no need to limit these jobs, there are only 358 of them
    para -ram=64g create jobList
    para try ... check ...
    para -maxJob=10 push
# Completed: 358 of 358 jobs
# CPU time in finished jobs:       5296s      88.27m     1.47h    0.06d  0.000 y
# IO & Wait Time:                   914s      15.23m     0.25h    0.01d  0.000 y
# Average job time:                  17s       0.29m     0.00h    0.00d
# Longest finished job:             404s       6.73m     0.11h    0.00d
# Submission to last job:           451s       7.52m     0.13h    0.01d

    du -hsc result
    #  156G    result

    # Load into database
    rm -f /gbdb/hg38/multiz30way/maf/*
    cd /hive/data/genomes/hg38/bed/multiz30way/anno/result

    ln -s `pwd`/*.maf /gbdb/hg38/multiz30way/maf/

    # this generates an immense multiz30way.tab file in the directory
    #	where it is running.  Best to run this over in scratch.
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/hg38/multiz30way/maf hg38 multiz30way
    # Loaded 40655883 mafs in 358 files from /gbdb/hg38/multiz30way/maf
    # real    37m27.075s

    # -rw-rw-r-- 1 2177747201 Nov  2 18:27 multiz30way.tab

    time (cat /gbdb/hg38/multiz30way/maf/*.maf \
        | hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 hg38 multiz30waySummary stdin)
# Created 4568973 summary blocks from 850984320 components and 40655883 mafs from stdin
# real    59m27.383s

# -rw-rw-r--   1 2177747201 Nov  2 18:27 multiz30way.tab
# -rw-rw-r--   1  224894681 Nov  3 08:12 multiz30waySummary.tab

    wc -l multiz30way*.tab
    # 40655883 multiz30way.tab
    #  4568973 multiz30waySummary.tab

    rm multiz30way*.tab

##############################################################################
# MULTIZ7WAY MAF FRAMES (DONE - 2017-11-03 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/hg38/bed/multiz30way/frames
    cd /hive/data/genomes/hg38/bed/multiz30way/frames
#   survey all the genomes to find out what kinds of gene tracks they have

    printf '#!/bin/csh -fe
foreach db (`cat ../species.list`)
    echo -n "# ${db}: "
    set tables = `hgsql $db -N -e "show tables" | egrep "Gene|ncbiRefSeq"`
    foreach table ($tables)
        if ($table == "ensGene" || $table == "refGene" || \
           $table == "ncbiRefSeq" || $table == "mgcGenes" || \
           $table == "knownGene" || $table == "xenoRefGene" ) then
           set count = `hgsql $db -N -e "select count(*) from $table"`
            echo -n "${table}: ${count}, "
        endif
    end
    echo
end
' > showGenes.csh

    chmod +x ./showGenes.csh
    time ./showGenes.csh
# hg38: ensGene: 208239, knownGene: 196838, mgcGenes: 35312, ncbiRefSeq: 159322, refGene: 74391, xenoRefGene: 186565,
# panTro5: refGene: 2901, xenoRefGene: 232448,
# panPan2: ncbiRefSeq: 59356, refGene: 130, xenoRefGene: 222742,
# gorGor5: refGene: 444, xenoRefGene: 315030,
# ponAbe2: ensGene: 29447, refGene: 3572, xenoRefGene: 329566,
# nomLeu3: xenoRefGene: 220286,
# rheMac8: ensGene: 56743, refGene: 6481, xenoRefGene: 223255,
# macFas5: refGene: 2164, xenoRefGene: 314695,
# macNem1: refGene: 64, xenoRefGene: 316886,
# cerAty1: refGene: 450, xenoRefGene: 492070,
# papAnu3: ensGene: 31109, refGene: 513, xenoRefGene: 324140,
# chlSab2: ensGene: 28078, xenoRefGene: 245054,
# manLeu1: refGene: 3, xenoRefGene: 456179,
# nasLar1: xenoRefGene: 360558,
# colAng1: ncbiRefSeq: 47349, refGene: 3, xenoRefGene: 332184,
# rhiRox1: xenoRefGene: 364268,
# rhiBie1: xenoRefGene: 342566,
# calJac3: ensGene: 55116, refGene: 228, xenoRefGene: 346395,
# saiBol1: xenoRefGene: 506909,
# cebCap1: refGene: 293, xenoRefGene: 457440,
# aotNan1: refGene: 17, xenoRefGene: 471455,
# tarSyr2: xenoRefGene: 349126,
# micMur3: xenoRefGene: 224817,
# proCoq1: xenoRefGene: 449845,
# eulMac1: xenoRefGene: 427352,
# eulFla1: xenoRefGene: 434365,
# otoGar3: ensGene: 28565, xenoRefGene: 470891,
# mm10: ensGene: 103734, knownGene: 63759, mgcGenes: 27612, ncbiRefSeq: 106520, refGene: 38421, xenoRefGene: 183274,
# canFam3: ensGene: 39074, refGene: 2297, xenoRefGene: 268480,
# dasNov3: ensGene: 37723, xenoRefGene: 500914,

# real    0m1.505s

    # from that summary, use these gene sets:
    # knownGene - hg38 mm10
    # ensGene - ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3
    # xenoRefGene -  panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1

    mkdir genes

    #   1. knownGene: hg38 mm10
    for DB in hg38 mm10
do
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > genes/${DB}.gp.gz
    genePredCheck -db=${DB} genes/${DB}.gp.gz 2>&1 | sed -e 's/^/    # /;'
done
    # checked: 21554 failed: 0
    # checked: 21100 failed: 0

    #   2. ensGene: ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3
    for DB in ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3
do
hgsql -N -e "select
name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds
from ensGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /dev/shm/${DB}.tmp.gz
    mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz
    echo -n "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# ponAbe2: checked: 20220 failed: 0
# rheMac8: checked: 20859 failed: 0
# papAnu3: checked: 19113 failed: 0
# chlSab2: checked: 19080 failed: 0
# calJac3: checked: 20827 failed: 0
# otoGar3: checked: 19472 failed: 0
# canFam3: checked: 19507 failed: 0
# dasNov3: checked: 22586 failed: 0

    #   3. xenoRefGene for panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1

    for DB in panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1
do
    hgsql -N -e "select
name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds
from xenoRefGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /dev/shm/${DB}.tmp.gz
    mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz
    echo -n "# ${DB}: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# panTro5: checked: 21593 failed: 0
# panPan2: checked: 20031 failed: 0
# gorGor5: checked: 24721 failed: 0
# nomLeu3: checked: 20028 failed: 0
# macFas5: checked: 24291 failed: 0
# macNem1: checked: 24281 failed: 0
# cerAty1: checked: 27975 failed: 0
# manLeu1: checked: 27196 failed: 0
# nasLar1: checked: 29765 failed: 0
# colAng1: checked: 24558 failed: 0
# rhiRox1: checked: 26354 failed: 0
# rhiBie1: checked: 26930 failed: 0
# saiBol1: checked: 26867 failed: 0
# cebCap1: checked: 29673 failed: 0
# aotNan1: checked: 30988 failed: 0
# tarSyr2: checked: 29235 failed: 0
# micMur3: checked: 20083 failed: 0
# proCoq1: checked: 25577 failed: 0
# eulMac1: checked: 26918 failed: 0
# eulFla1: checked: 27223 failed: 0

    # verify counts for genes are reasonable:
    for T in genes/*.gz
do
    echo -n "# $T: "
    zcat $T | cut -f1 | sort | uniq -c | wc -l
done
# genes/aotNan1.gp.gz: 26592
# genes/calJac3.gp.gz: 20827
# genes/canFam3.gp.gz: 19507
# genes/cebCap1.gp.gz: 25680
# genes/cerAty1.gp.gz: 24658
# genes/chlSab2.gp.gz: 19080
# genes/colAng1.gp.gz: 22290
# genes/dasNov3.gp.gz: 22586
# genes/eulFla1.gp.gz: 24120
# genes/eulMac1.gp.gz: 23994
# genes/gorGor5.gp.gz: 22552
# genes/hg38.gp.gz: 21554
# genes/macFas5.gp.gz: 22206
# genes/macNem1.gp.gz: 22243
# genes/manLeu1.gp.gz: 24280
# genes/micMur3.gp.gz: 19472
# genes/mm10.gp.gz: 21100
# genes/nasLar1.gp.gz: 25793
# genes/nomLeu3.gp.gz: 19509
# genes/otoGar3.gp.gz: 19472
# genes/panPan2.gp.gz: 19596
# genes/panTro5.gp.gz: 20327
# genes/papAnu3.gp.gz: 19113
# genes/ponAbe2.gp.gz: 20220
# genes/proCoq1.gp.gz: 23134
# genes/rheMac8.gp.gz: 20859
# genes/rhiBie1.gp.gz: 23979
# genes/rhiRox1.gp.gz: 23570
# genes/saiBol1.gp.gz: 23863
# genes/tarSyr2.gp.gz: 25017


    # kluster job to annotate each maf file
    screen -S hg38      # manage long running procedure with screen
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz30way/frames

    printf '#!/bin/csh -fe

set C = $1
set G = $2

cat ../maf/${C}.maf | genePredToMafFrames hg38 stdin stdout \
        ${G} genes/${G}.gp.gz | gzip > parts/${C}.${G}.mafFrames.gz
' > runOne

    chmod +x runOne

    ls ../maf | sed -e "s/.maf//" > chr.list
    ls genes | sed -e "s/.gp.gz//" > gene.list

    printf '#LOOP
runOne $(root1) $(root2) {check out exists+ parts/$(root1).$(root2).mafFrames.gz}
#ENDLOOP
' > template

    mkdir parts
    gensub2 chr.list gene.list template jobList
    para -ram=64g create jobList
    para try ... check ... push
# Completed: 10740 of 10740 jobs
# CPU time in finished jobs:      39407s     656.78m    10.95h    0.46d  0.001 y
# IO & Wait Time:                 27424s     457.07m     7.62h    0.32d  0.001 y
# Average job time:                   6s       0.10m     0.00h    0.00d
# Longest finished job:             360s       6.00m     0.10h    0.00d
# Submission to last job:           881s      14.68m     0.24h    0.01d

    # collect all results into one file:
    cd /hive/data/genomes/hg38/bed/multiz30way/frames
    time find ./parts -type f | while read F
do
    echo "${F}" 1>&2
    zcat ${F}
done | sort -k1,1 -k2,2n > multiz30wayFrames.bed
    # real    2m4.953s

    # -rw-rw-r-- 1 468491708 Nov  3 10:30 multiz30wayFrames.bed

    gzip multiz30wayFrames.bed

    # verify there are frames on everything, should be 46 species:
    # (count from: ls genes | wc)
    zcat multiz30wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \
        | sed -e 's/^/# /;' > species.check.list
    wc -l species.check.list
    # 30

#  256062 aotNan1
#  246852 calJac3
#  274139 canFam3
#  251294 cebCap1
#  258355 cerAty1
#  214185 chlSab2
#  244719 colAng1
#  264484 dasNov3
#  210815 eulFla1
#  213386 eulMac1
#  287686 gorGor5
#  209184 hg38
#  253170 macFas5
#  257891 macNem1
#  248164 manLeu1
#  215472 micMur3
#  260934 mm10
#  187651 nasLar1
#  230776 nomLeu3
#  249009 otoGar3
#  223118 panPan2
#  223812 panTro5
#  193979 papAnu3
#  200343 ponAbe2
#  210398 proCoq1
#  228189 rheMac8
#  239047 rhiBie1
#  223257 rhiRox1
#  248138 saiBol1
#  222251 tarSyr2

    #   load the resulting file
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/frames
    time hgLoadMafFrames hg38 multiz30wayFrames multiz30wayFrames.bed.gz
    #   real    1m13.122s

    hgsql -e 'select count(*) from multiz30wayFrames;' hg38
    # +----------+
    # | count(*) |
    # +----------+
    # |  7046760 |
    # +----------+

    time featureBits -countGaps hg38 multiz30wayFrames
    # 55160112 bases of 3209286105 (1.719%) in intersection
    # real    0m44.816s

    #   enable the trackDb entries:
# frames multiz30wayFrames
# irows on
    #   zoom to base level in an exon to see codon displays
    #	appears to work OK

#########################################################################
# Phylogenetic tree from 30-way (DONE - 2013-09-13 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/multiz30way/4d
    cd /hive/data/genomes/hg38/bed/multiz30way/4d

    # the annotated maf's are in:
    ../anno/result/*.maf

    # using knownGene for hg38, only transcribed genes and nothing
    #	from the randoms and other misc.
    hgsql -Ne "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene where cdsEnd > cdsStart;" hg38 \
      | egrep -E -v "chrM|chrUn|random|_alt" > knownGene.gp
    wc -l *.gp
    #     95199 knownGene.gp

    # verify it is only on the chroms:
    cut -f2 knownGene.gp | sort | uniq -c | sort -rn | sed -e 's/^/    # /;'
    #    7956 chr1
    #    7306 chr19
    #    6554 chr17
    #    6371 chr11
    #    6301 chr2
    #    5794 chr12
    #    5688 chr3
    #    4971 chr16
    #    4324 chr7
    #    4277 chr6
    #    4108 chr5
    #    3751 chr14
    #    3622 chr4
    #    3580 chr8
    #    3364 chr15
    #    3076 chrX
    #    2968 chr10
    #    2961 chr9
    #    2107 chr22
    #    2091 chr20
    #    1703 chr18
    #    1175 chr13
    #     935 chr21
    #     216 chrY

    genePredSingleCover knownGene.gp stdout | sort > knownGeneNR.gp
    wc -l knownGeneNR.gp
    #	19306 knownGeneNR.gp

    ssh ku
    mkdir /hive/data/genomes/hg38/bed/multiz30way/4d/run
    cd /hive/data/genomes/hg38/bed/multiz30way/4d/run
    mkdir ../mfa

    # newer versions of msa_view have a slightly different operation
    # the sed of the gp file inserts the reference species in the chr name
    cat << '_EOF_' > 4d.csh
#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set r = "/hive/data/genomes/hg38/bed/multiz30way"
set c = $1
set infile = $r/anno/result/$2
set outfile = $3
cd /dev/shm
# 'clean' maf, removes all chrom names, leaves only the db name
perl -wpe 's/^s ([^.]+)\.\S+/s $1/' $infile > $c.maf
awk -v C=$c '$2 == C {print}' $r/4d/knownGeneNR.gp | sed -e "s/\t$c\t/\thg38.$c\t/" > $c.gp
set NL=`wc -l $c.gp| gawk '{print $1}'`
if ("$NL" != "0") then
    $PHASTBIN/msa_view --4d --features $c.gp -i MAF $c.maf -o SS > $c.ss
    $PHASTBIN/msa_view -i SS --tuple-size 1 $c.ss > $r/4d/run/$outfile
else
    echo "" > $r/4d/run/$outfile
endif
rm -f $c.gp $c.maf $c.ss
'_EOF_'
    # << happy emacs
    chmod +x 4d.csh

    ls -1S /hive/data/genomes/hg38/bed/multiz30way/anno/result/*.maf \
	| sed -e "s#.*multiz30way/anno/result/##" \
        | egrep -E -v "chrM|chrUn|random|_alt" > maf.list

    printf '#LOOP
4d.csh $(root1) $(path1) {check out line+ ../mfa/$(root1).mfa}
#ENDLOOP
' > template

    gensub2 maf.list single template jobList
    para -ram=64g create jobList
    para try ... check ... push ... etc...
    para time
# Completed: 24 of 24 jobs
# CPU time in finished jobs:       7202s     120.03m     2.00h    0.08d  0.000 y
# IO & Wait Time:                   480s       8.00m     0.13h    0.01d  0.000 y
# Average job time:                 320s       5.33m     0.09h    0.00d
# Longest finished job:             706s      11.77m     0.20h    0.01d
# Submission to last job:           718s      11.97m     0.20h    0.01d

    # combine mfa files
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/4d
    # verify no tiny files:
    ls -og mfa | sort -k3nr | tail -2
    #  -rw-rw-r-- 1  235884 Nov  3 11:25 chrY.mfa

    #want comma-less species.list
    time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_view \
	--aggregate "`cat ../species.list`" mfa/*.mfa | sed s/"> "/">"/ \
	    > 4d.all.mfa
    # real    0m3.182s

    # check they are all in there:
    grep "^>" 4d.all.mfa | wc -l
    #   30

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        hg38.30way.nh

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	../hg38.30way.nh > tree-commas.nh

    # use phyloFit to create tree model (output is phyloFit.mod)
    time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/phyloFit \
	    --EM --precision MED --msa-format FASTA --subst-mod REV \
		--tree tree-commas.nh 4d.all.mfa
    #   real    8m6.444s

    mv phyloFit.mod all.mod

    grep TREE all.mod
# ((((((((((((hg38:0.0101811,panTro5:0.00256557):0.00168527,
# panPan2:0.00255779):0.00567544,gorGor5:0.00857055):0.0093291,
# ponAbe2:0.0183757):0.00328934,nomLeu3:0.022488):0.0111201,
# (((((rheMac8:0.00266214,(macFas5:0.00218171,
# macNem1:0.00424092):0.00171674):0.00606702,cerAty1:0.00671556):0.00164923,
# papAnu3:0.00691761):0.00171877,(chlSab2:0.0163497,
# manLeu1:0.00699129):0.00165863):0.00933639,((nasLar1:0.00768293,
# colAng1:0.0163932):0.00167418,(rhiRox1:0.00213201,
# rhiBie1:0.00222829):0.00577271):0.0104228):0.0214064):0.0206136,
# (((calJac3:0.0358464,saiBol1:0.0324064):0.00173657,
# cebCap1:0.0283117):0.00202114,aotNan1:0.0232387):0.0378592):0.0606754,
# tarSyr2:0.142222):0.011174,(((micMur3:0.0563648,
# proCoq1:0.0388184):0.00530425,(eulMac1:0.00218443,
# eulFla1:0.00228562):0.0410542):0.0370791,
# otoGar3:0.132725):0.0335535):0.0178619,mm10:0.344583):0.0241482,
# canFam3:0.163902):0.0880829,dasNov3:0.0880829);

    # compare these calculated lengths to what we started with

    /cluster/bin/phast/all_dists ../hg38.30way.nh  | grep hg38 \
	| sed -e "s/hg38.//;" | sort > original.dists

    grep TREE all.mod | sed -e 's/TREE: //;' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep hg38 \
          | sed -e "s/hg38.//;"  | sort > hg38.dists

    # printing out the 'original', the 'new' the 'difference' and
    #    percent difference/delta
    join original.dists hg38.dists | awk '{
  printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%8.6f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }'       | sort -k4n
#       panTro5 0.013390        0.012747        0.000643        5.044324
#       panPan2 0.015610        0.014424        0.001186        8.222407
#       gorGor5 0.019734        0.026112        -0.006378       -24.425551
#       ponAbe2 0.039403        0.045247        -0.005844       -12.915773
#       nomLeu3 0.046204        0.052648        -0.006444       -12.239781
#       papAnu3 0.079626        0.080660        -0.001034       -1.281924
#       manLeu1 0.090974        0.080673        0.010301        12.768832
#       rhiRox1 0.075474        0.081014        -0.005540       -6.838324
#       rhiBie1 0.075474        0.081111        -0.005637       -6.949736
#       cerAty1 0.082584        0.082107        0.000477        0.580949
#       nasLar1 0.075474        0.082467        -0.006993       -8.479756
#       rheMac8 0.079575        0.084120        -0.004545       -5.402996
#       macFas5 0.079575        0.085357        -0.005782       -6.773903
#       macNem1 0.081584        0.087416        -0.005832       -6.671548
#       chlSab2 0.087974        0.090031        -0.002057       -2.284769
#       colAng1 0.075574        0.091177        -0.015603       -17.112868
#       aotNan1 0.102804        0.122992        -0.020188       -16.414076
#       cebCap1 0.108804        0.130086        -0.021282       -16.359946
#       saiBol1 0.087804        0.135917        -0.048113       -35.398810
#       calJac3 0.107454        0.139357        -0.031903       -22.893001
#       eulMac1 0.190934        0.247615        -0.056681       -22.890778
#       eulFla1 0.190934        0.247716        -0.056782       -22.922217
#       proCoq1 0.230934        0.248499        -0.017565       -7.068439
#       tarSyr2 0.221294        0.264791        -0.043497       -16.426918
#       micMur3 0.236534        0.266045        -0.029511       -11.092484
#       otoGar3 0.270334        0.300022        -0.029688       -9.895274
#       canFam3 0.332429        0.339655        -0.007226       -2.127453
#       dasNov3 0.366691        0.351919        0.014772        4.197557
#       mm10    0.502391        0.496188        0.006203        1.250131

#########################################################################
# phastCons 30-way (DONE - 2015-05-07 - Hiram)
    # split 30way mafs into 10M chunks and generate sufficient statistics
    # files for # phastCons
    ssh ku
    mkdir -p /hive/data/genomes/hg38/bed/multiz30way/cons/ss
    mkdir -p /hive/data/genomes/hg38/bed/multiz30way/cons/msa.split
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/msa.split

    cat << '_EOF_' > doSplit.csh
#!/bin/csh -ef
set c = $1
set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf
set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/cons/ss/$c
set WC = `cat $MAF | wc -l`
set NL = `grep "^#" $MAF | wc -l`
if ( -s $2 ) then
    exit 0
endif
if ( -s $2.running ) then
    exit 0
endif

date >> $2.running

rm -fr $WINDOWS
mkdir $WINDOWS
pushd $WINDOWS > /dev/null
if ( $WC != $NL ) then
/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \
    $MAF -i MAF -o SS -r $WINDOWS/$c -w 3000000,0 -I 300 -B 5000
endif
popd > /dev/null
date >> $2
rm -f $2.running
'_EOF_'
    # << happy emacs
    chmod +x doSplit.csh

    cat << '_EOF_' > template
    printf '#LOOP
doSplit.csh $(root1) {check out line+ $(root1).done}
#ENDLOOP
' > template

F_' > doSplit.csh
#!/bin/csh -ef
set c = $1
set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf
set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/cons/ss/$c
set WC = `cat $MAF | wc -l`
set NL = `grep "^#" $MAF | wc -l`
if ( -s $2 ) then
    exit 0
endif
if ( -s $2.running ) then
    exit 0
endif

date >> $2.running

rm -fr $WINDOWS
mkdir $WINDOWS
pushd $WINDOWS > /dev/null
if ( $WC != $NL ) then
/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \
    $MAF -i MAF -o SS -r $WINDOWS/$c -w 3000000,0 -I 300 -B 5000
endif
popd > /dev/null
date >> $2
rm -f $2.running
'_EOF_'
    # << happy emacs
    chmod +x doSplit.csh

    cat << '_EOF_' > template
#LOOP
doSplit.csh $(root1) {check out line+ $(root1).done}
#ENDLOOP

#	do the easy ones first to see some immediate results
    ls -1S -r ../../anno/result | sed -e "s/.maf//;" > maf.list
    # all can finish OK at a 64Gb memory limit
    gensub2 maf.list single template jobList
    para -ram=64g create jobList
    para try ... check ... etc
    para push
# Completed: 358 of 358 jobs
# CPU time in finished jobs:      13099s     218.32m     3.64h    0.15d  0.000 y
# IO & Wait Time:                  1841s      30.68m     0.51h    0.02d  0.000 y
# Average job time:                  42s       0.70m     0.01h    0.00d
# Longest finished job:            1393s      23.22m     0.39h    0.02d
# Submission to last job:          1468s      24.47m     0.41h    0.02d

    # Run phastCons
    #	This job is I/O intensive in its output files, beware where this
    #	takes place or do not run too many at once.
    ssh ku
    mkdir -p /hive/data/genomes/hg38/bed/multiz30way/cons/run.cons
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/run.cons

    #	This is setup for multiple runs based on subsets, but only running
    #   the 'all' subset here.
    #   It triggers off of the current working directory
    #	$cwd:t which is the "grp" in this script.  Running:
    #	all and vertebrates

    cat << '_EOF_' > doPhast.csh
#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set c = $1
set f = $2
set len = $3
set cov = $4
set rho = $5
set grp = $cwd:t
set cons = /hive/data/genomes/hg38/bed/multiz30way/cons
set tmp = $cons/tmp/$f
mkdir -p $tmp
set ssSrc = $cons/ss
set useGrp = "$grp.mod"
if (-s $cons/$grp/$grp.non-inf) then
  ln -s $cons/$grp/$grp.mod $tmp
  ln -s $cons/$grp/$grp.non-inf $tmp
  ln -s $ssSrc/$c/$f.ss $tmp
else
  ln -s $ssSrc/$c/$f.ss $tmp
  ln -s $cons/$grp/$grp.mod $tmp
endif
pushd $tmp > /dev/null
if (-s $grp.non-inf) then
  $PHASTBIN/phastCons $f.ss $useGrp \
    --rho $rho --expected-length $len --target-coverage $cov --quiet \
    --not-informative `cat $grp.non-inf` \
    --seqname $c --idpref $c --most-conserved $f.bed --score > $f.pp
else
  $PHASTBIN/phastCons $f.ss $useGrp \
    --rho $rho --expected-length $len --target-coverage $cov --quiet \
    --seqname $c --idpref $c --most-conserved $f.bed --score > $f.pp
endif
popd > /dev/null
mkdir -p pp/$c bed/$c
sleep 4
touch pp/$c bed/$c
rm -f pp/$c/$f.pp
rm -f bed/$c/$f.bed
mv $tmp/$f.pp pp/$c
mv $tmp/$f.bed bed/$c
rm -fr $tmp
'_EOF_'
    # << happy emacs
    chmod +x doPhast.csh

    #	this template will serve for all runs
    #	root1 == chrom name, file1 == ss file name without .ss suffix
    printf '#LOOP
../run.cons/doPhast.csh $(root1) $(file1) 45 0.3 0.3 {check out line+ pp/$(root1)/$(file1).pp}
#ENDLOOP
' > template

    ls -1S ../ss/chr*/chr* | sed -e "s/.ss$//" > ss.list
    wc -l ss.list
    #	1337 ss.list

    # Create parasol batch and run it
    # run for all species
    cd /hive/data/genomes/hg38/bed/multiz30way/cons
    mkdir -p all
    cd all
    #	Using the .mod tree
    cp -p ../../4d/all.mod ./all.mod

    gensub2 ../run.cons/ss.list single ../run.cons/template jobList
    # beware overwhelming the cluster with these fast running high I/O jobs
    para -ram=32g create jobList
    para try ... check ...
    para -maxJob=16 push
# Completed: 1337 of 1337 jobs
# CPU time in finished jobs:      17323s     288.72m     4.81h    0.20d  0.001 y
# IO & Wait Time:                  9727s     162.11m     2.70h    0.11d  0.000 y
# Average job time:                  20s       0.34m     0.01h    0.00d
# Longest finished job:              31s       0.52m     0.01h    0.00d
# Submission to last job:           230s       3.83m     0.06h    0.00d

    # create Most Conserved track
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/all
    time cut -f1 ../../../../chrom.sizes | while read C
do
    echo $C 1>&2
    ls -d bed/${C} 2> /dev/null | while read D
    do
        cat ${D}/${C}*.bed
    done | sort -k1,1 -k2,2n \
    | awk '{printf "%s\t%d\t%d\tlod=%d\t%s\n", "'${C}'", $2, $3, $5, $5;}'
done > tmpMostConserved.bed
    # real    0m50.678s

    # -rw-rw-r--   1 101245734 Nov  3 14:20 tmpMostConserved.bed

    time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \
        > mostConserved.bed
    # real    0m24.196s

    # -rw-rw-r--   1 103966297 Nov  3 14:21 mostConserved.bed

    # load into database
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/all
    time hgLoadBed hg38 phastConsElements30way mostConserved.bed
    #  Read 2949865 elements of size 5 from mostConserved.bed
    #  real    0m26.263s

    #	--rho 0.3 --expected-length 45 --target-coverage 0.3
    time featureBits hg38 -enrichment knownGene:cds phastConsElements30way
# knownGene:cds 1.271%, phastConsElements30way 5.795%, both 0.874%, cover 68.73%, enrich 11.86x
# real    0m21.637s

    # Try for 5% overall cov, and 70% CDS cov
    time featureBits hg38 -enrichment refGene:cds phastConsElements30way
# refGene:cds 1.225%, phastConsElements30way 5.795%, both 0.863%, cover 70.50%, enrich 12.16x

# real    0m22.260s

    # Create merged posterier probability file and wiggle track data files
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/all
    mkdir downloads

    time for D in `ls -d pp/chr* | sed -e 's#pp/##'`
do
    echo "working: $D" 1>&2
    find ./pp/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \
	| sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \
        | gzip -c > downloads/${D}.phastCons30way.wigFix.gz
done
    # real    32m29.089s


    #	encode those files into wiggle data
    time (zcat downloads/*.wigFix.gz \
	| wigEncode stdin phastCons30way.wig phastCons30way.wib)
    #   Converted stdin, upper limit 1.00, lower limit 0.00
    #   real    15m40.010s

    du -hsc *.wi?
    # 2.8G    phastCons30way.wib
    # 283M    phastCons30way.wig

    #	encode into a bigWig file:
    #	(warning wigToBigWig process may be too large for memory limits
    #	in bash, to avoid the 32 Gb memory limit, set 180 Gb here:
export sizeG=188743680
ulimit -d $sizeG
ulimit -v $sizeG
    time (zcat downloads/*.wigFix.gz \
      | wigToBigWig -verbose=2 stdin \
	../../../../chrom.sizes phastCons30way.bw) > bigWig.log 2>&1
    egrep "VmPeak|real" bigWig.log
    # pid=37111: VmPeak:    33886864 kB
    # real    42m13.614s

    # -rw-rw-r--   1 7077152013 Nov  6 08:52 phastCons30way.bw


    bigWigInfo phastCons30way.bw
version: 4
isCompressed: yes
isSwapped: 0
primaryDataSize: 5,097,637,987
primaryIndexSize: 93,372,648
zoomLevels: 10
chromCount: 355
basesCovered: 2,955,660,600
mean: 0.128025
min: 0.000000
max: 1.000000
std: 0.247422

    #	if you wanted to use the bigWig file, loading bigWig table:
    #   but we don't use the bigWig file
    mkdir /gbdb/hg38/bbi
    ln -s `pwd`/phastCons30way.bw /gbdb/hg38/bbi
    hgsql hg38 -e 'drop table if exists phastCons30way; \
            create table phastCons30way (fileName varchar(255) not null); \
            insert into phastCons30way values
	("/gbdb/hg38/bbi/phastCons30way.bw");'

    # Load gbdb and database with wiggle.
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/all
    ln -s `pwd`/phastCons30way.wib /gbdb/hg38/multiz30way/phastCons30way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz30way hg38 \
	phastCons30way phastCons30way.wig
    #   real    0m32.272s

    time wigTableStats.sh hg38 phastCons30way
# db.table            min max   mean       count     sumData
# hg38.phastCons30way     0 1 0.128025 2955660600 3.78397e+08
#       stdDev viewLimits
#     0.247422 viewLimits=0:1
# real    0m13.507s

    #  Create histogram to get an overview of all the data
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz30way/cons/all
    time hgWiggle -doHistogram -db=hg38 \
	-hBinSize=0.001 -hBinCount=300 -hMinVal=0.0 -verbose=2 \
	    phastCons30way > histogram.data 2>&1
    #	real    2m38.952s

    #	create plot of histogram:

    printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \
"/usr/share/fonts/default/Type1/n022004l.pfb"
set size 1.4, 0.8
set key left box
set grid noxtics
set grid ytics
set title " Human Hg38 Histogram phastCons30way track"
set xlabel " phastCons30way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set yrange [0:0.02]

plot "histogram.data" using 2:5 title " RelFreq" with impulses, \
        "histogram.data" using 2:7 axes x1y2 title " CRF" with lines
' | gnuplot > histo.png

    # take a look to see if it is sane:

    display histo.png &

#########################################################################
# phyloP for 30-way (DONE - 2017-11-06 - Hiram)
#
    # split SS files into 1M chunks, this business needs smaller files
    #   to complete

    ssh ku
    mkdir /hive/data/genomes/hg38/bed/multiz30way/consPhyloP
    cd /hive/data/genomes/hg38/bed/multiz30way/consPhyloP
    mkdir ss run.split
    cd run.split

    printf '#!/bin/csh -ef
set c = $1
set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf
set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/consPhyloP/ss/$c
set WC = `cat $MAF | wc -l`
set NL = `grep "^#" $MAF | wc -l`
if ( -s $2 ) then
    exit 0
endif
if ( -s $2.running ) then
    exit 0
endif

date >> $2.running

rm -fr $WINDOWS
mkdir -p $WINDOWS
pushd $WINDOWS > /dev/null
if ( $WC != $NL ) then
/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \
    $MAF -i MAF -o SS -r $WINDOWS/$c -w 1000000,0 -I 1000 -B 5000
endif
popd > /dev/null
date >> $2
rm -f $2.running
' > doSplit.csh

    chmod +x doSplit.csh

    #	do the easy ones first to see some immediate results
    ls -1S -r ../../anno/result | sed -e "s/.maf//;" > maf.list

    # this needs a {check out line+ $(root1.done)} test for verification:
    printf '#LOOP
./doSplit.csh $(root1) $(root1).done
#ENDLOOP
' > template

    gensub2 maf.list single template jobList
    # all can complete successfully at the 64Gb memory limit
    para -ram=64g create jobList
    para try ... check ... push ... etc...

# Completed: 358 of 358 jobs
# CPU time in finished jobs:      13512s     225.20m     3.75h    0.16d  0.000 y
# IO & Wait Time:                  1646s      27.43m     0.46h    0.02d  0.000 y
# Average job time:                  42s       0.71m     0.01h    0.00d
# Longest finished job:            1494s      24.90m     0.41h    0.02d
# Submission to last job:          1717s      28.62m     0.48h    0.02d

    # run phyloP with score=LRT
    ssh ku
    mkdir /cluster/data/hg38/bed/multiz30way/consPhyloP
    cd /cluster/data/hg38/bed/multiz30way/consPhyloP

    mkdir run.phyloP
    cd run.phyloP
    # Adjust model file base composition background and rate matrix to be
    # representative of the chromosomes in play
    grep BACK ../../4d/all.mod
    #   BACKGROUND: 0.207173 0.328301 0.237184 0.227343

    grep BACKGROUND ../../4d/all.mod | awk '{printf "%0.3f\n", $3 + $4}'
    #	0.565
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../4d/all.mod 0.565 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #   BACKGROUND: 0.217500 0.282500 0.282500 0.217500

    printf '#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set f = $1
set ssFile = $1:t
set out = $2
set cName = $f:h
set n = $f:r:e
set grp = $cwd:t
set cons = /hive/data/genomes/hg38/bed/multiz30way/consPhyloP
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "$cons/ss/$cName/$ssFile"
set useGrp = "$grp.mod"
/bin/ln -s $cons/run.phyloP/$grp.mod $tmp
pushd $tmp > /dev/null
echo source: $ssSrc.ss
$PHASTBIN/phyloP --method LRT --mode CONACC --wig-scores --chrom $cName \
    -i SS $useGrp $ssSrc.ss > $ssFile.wigFix
popd > /dev/null
/bin/mkdir -p $out:h
sleep 4
/bin/touch $out:h
/bin/mv $tmp/$ssFile.wigFix $out
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp
' > doPhyloP.csh

    chmod +x doPhyloP.csh

    # Create list of chunks
    find ../ss -type f | sed -e "s/.ss$//; s#../ss/##;" > ss.list
    # make sure the list looks good
    wc -l ss.list
    #	3308 ss.list

    # Create template file
    #	file1 == $chr/$chunk/file name without .ss suffix
    printf '#LOOP
../run.phyloP/doPhyloP.csh $(path1) {check out line+ wigFix/$(dir1)/$(file1).wigFix}
#ENDLOOP
' > template

    ######################   Running all species  #######################
    # setup run for all species
    mkdir /hive/data/genomes/hg38/bed/multiz30way/consPhyloP/all
    cd /hive/data/genomes/hg38/bed/multiz30way/consPhyloP/all
    rm -fr wigFix
    mkdir wigFix

    gensub2 ../run.phyloP/ss.list single ../run.phyloP/template jobList
    # beware overloading the cluster with these quick and high I/O jobs
    para -ram=32g create jobList
    para try ... check ...
    para -maxJob=16 push
    para time > run.time

# Completed: 3308 of 3308 jobs
# CPU time in finished jobs:     647954s   10799.23m   179.99h    7.50d  0.021 y
# IO & Wait Time:                 22374s     372.90m     6.22h    0.26d  0.001 y
# Average job time:                 203s       3.38m     0.06h    0.00d
# Longest finished job:             349s       5.82m     0.10h    0.00d
# Submission to last job:          3226s      53.77m     0.90h    0.04d

    mkdir downloads
    time for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'`
do
    echo "working: $D" 1>&2
    find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \
	| sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \
        | gzip -c > downloads/${D}.phyloP30way.wigFix.gz
done
    #   real    48m50.219s

    du -hsc downloads
    #   4.6G    downloads

    # check integrity of data with wigToBigWig
    time (zcat downloads/*.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/hg38/chrom.sizes \
	phyloP30way.bw) > bigWig.log 2>&1


    egrep "real|VmPeak" bigWig.log
    # pid=66292: VmPeak:    33751268 kB
    #  real    43m40.194s


    bigWigInfo phyloP30way.bw  | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 6,304,076,591
# primaryIndexSize: 93,404,704
# zoomLevels: 10
# chromCount: 355
# basesCovered: 2,955,660,581
# mean: 0.097833
# min: -20.000000
# max: 1.312000
# std: 0.727453

    #	encode those files into wiggle data
    time (zcat downloads/*.wigFix.gz \
	| wigEncode stdin phyloP30way.wig phyloP30way.wib)

# Converted stdin, upper limit 1.31, lower limit -20.00
# real    17m36.880s
# -rw-rw-r--   1 2955660581 Nov  6 14:10 phyloP30way.wib
# -rw-rw-r--   1  304274846 Nov  6 14:10 phyloP30way.wig

    du -hsc *.wi?
    # 2.8G    phyloP30way.wib
    # 291M    phyloP30way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloP30way.wib /gbdb/hg38/multiz30way/phyloP30way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz30way hg38 \
	phyloP30way phyloP30way.wig
    # real    0m30.538s

    # use to set trackDb.ra entries for wiggle min and max
    # and verify table is loaded correctly

    wigTableStats.sh hg38 phyloP30way
# db.table          min   max     mean       count     sumData
# hg38.phyloP30way  -20 1.312 0.0978331 2955660581 2.89162e+08
#       stdDev viewLimits
#     0.727453 viewLimits=-3.53943:1.312

    #	that range is: 20+1.312= 21.312 for hBinSize=0.021312

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram \
	-hBinSize=0.021312 -hBinCount=1000 -hMinVal=-20 -verbose=2 \
	    -db=hg38 phyloP30way > histogram.data 2>&1
    #   real    2m43.313s

    # xaxis range:
    grep -v chrom histogram.data | grep "^[0-9]" | ave -col=2 stdin \
	| sed -e 's/^/# /;'
# Q1 -10.953050
# median -6.861155
# Q3 -2.769245
# average -6.875971
# min -20.000000
# max 1.312000
# count 768
# total -5280.745380
# standard deviation 4.757034

    # find out the range for the 2:5 graph
    grep -v chrom histogram.data | grep "^[0-9]" | ave -col=5 stdin \
      | sed -e 's/^/# /;'
# Q1 0.000000
# median 0.000001
# Q3 0.000140
# average 0.001302
# min 0.000000
# max 0.023556
# count 768
# total 0.999975
# standard deviation 0.003490

    #	create plot of histogram:
    printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \
"/usr/share/fonts/default/Type1/n022004l.pfb"
set size 1.4, 0.8
set key left box
set grid noxtics
set grid ytics
set title " Human hg38 Histogram phyloP30way track"
set xlabel " phyloP30way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set xrange [-5:1.5]
set yrange [0:0.04]

plot "histogram.data" using 2:5 title " RelFreq" with impulses, \
        "histogram.data" using 2:7 axes x1y2 title " CRF" with lines
' | gnuplot > histo.png

    # verify it looks sane
    display histo.png &

#############################################################################
# construct download files for 30-way (TBD - 2015-04-15 - Hiram)
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way
    mkdir /hive/data/genomes/hg38/bed/multiz30way/downloads
    cd /hive/data/genomes/hg38/bed/multiz30way/downloads
    mkdir multiz30way phastCons30way phyloP30way

    #########################################################################
    ## create upstream refGene maf files
    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/multiz30way
    # bash script

#!/bin/sh
export geneTbl="refGene"
for S in 300 2000 5000
do
    echo "making upstream${S}.maf"
    featureBits hg38 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \
        | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \
        | /cluster/bin/$MACHTYPE/mafFrags hg38 multiz30way \
                stdin stdout \
                -orgs=/hive/data/genomes/hg38/bed/multiz30way/species.list \
        | gzip -c > upstream${S}.${geneTbl}.maf.gz
    echo "done upstream${S}.${geneTbl}.maf.gz"
done

    #   real    88m40.730s

-rw-rw-r-- 1   52659159 Nov  6 11:46 upstream300.knownGene.maf.gz
-rw-rw-r-- 1  451126665 Nov  6 12:15 upstream2000.knownGene.maf.gz
-rw-rw-r-- 1 1080533794 Nov  6 12:55 upstream5000.knownGene.maf.gz

    ######################################################################
    ## compress the maf files
    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/multiz30way
    mkdir maf
    rsync -a -P ../../anno/result/ ./maf/
    du -hsc maf/
    # 156G    maf
    cd maf
    time gzip *.maf &
    # real    135m1.784s

    du -hscL maf ../../anno/result/
    #  18G     maf

    cd maf
    md5sum *.maf.gz *.nh > md5sum.txt

    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/maf
    cd maf
    ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/maf
    cd --
    ln -s `pwd`/*.maf.gz `pwd`/*.nh `pwd`/*.txt \
         /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/

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

    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/multiz30way
    grep TREE ../../4d/all.mod | awk '{print $NF}' \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > hg38.30way.nh
    ~/kent/src/hg/utils/phyloTrees/commonNames.sh hg38.30way.nh \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > hg38.30way.commonNames.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh hg38.30way.nh \
	| $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
	    > hg38.30way.scientificNames.nh
    time md5sum *.nh *.maf.gz > md5sum.txt
    #   real    0m3.147s

    ln -s `pwd`/*.maf.gz `pwd`/*.nh \
        /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way

    du -hsc ./maf ../../anno/result
    #  18G     ./maf
    # 156G    ../../anno/result

    # obtain the README.txt from hg38/multiz20way and update for this
    #   situation
    ln -s `pwd`/*.txt \
         /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/

    #####################################################################
    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phastCons30way

    mkdir hg38.30way.phastCons
    cd hg38.30way.phastCons
    ln -s ../../../cons/all/downloads/*.wigFix.gz .
    md5sum *.gz > md5sum.txt

    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phastCons30way
    ln -s ../../cons/all/phastCons30way.bw ./hg38.phastCons30way.bw
    ln -s ../../cons/all/all.mod ./hg38.phastCons30way.mod
    time md5sum *.mod *.bw > md5sum.txt
    #   real    0m20.354s

    # obtain the README.txt from hg38/phastCons20way and update for this
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way/hg38.30way.phastCons
    cd hg38.30way.phastCons
    ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way/hg38.30way.phastCons

    cd ..
    #   situation
    ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \
      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way

    #####################################################################
    cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phyloP30way

    mkdir hg38.30way.phyloP
    cd hg38.30way.phyloP

    ln -s ../../../consPhyloP/all/downloads/*.wigFix.gz .
    md5sum *.wigFix.gz > md5sum.txt

    cd ..

    ln -s ../../consPhyloP/run.phyloP/all.mod hg38.phyloP30way.mod
    ln -s ../../consPhyloP/all/phyloP30way.bw hg38.phyloP30way.bw

    md5sum *.mod *.bw > md5sum.txt

    # obtain the README.txt from hg38/phyloP20way and update for this
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way/hg38.30way.phyloP
    cd hg38.30way.phyloP
    ln -s `pwd`/* \
/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way/hg38.30way.phyloP

    cd ..

    #   situation
    ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \
      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way

#############################################################################
# hgPal downloads (DONE - 2017-11-06 - Hiram)
#   FASTA from 30-way for knownGene, refGene and knownCanonical

    ssh hgwdev
    screen -S hg38HgPal
    mkdir /hive/data/genomes/hg38/bed/multiz30way/pal
    cd /hive/data/genomes/hg38/bed/multiz30way/pal
    cat ../species.list | tr '[ ]' '[\n]' > order.list

    ### knownCanonical with full CDS
    cd /hive/data/genomes/hg38/bed/multiz30way/pal
    export mz=multiz30way
    export gp=knownCanonical
    export db=hg38
    mkdir exonAA exonNuc knownCanonical

    time cut -f1 ../../../chrom.sizes | while read C
    do
        echo $C 1>&2
	hgsql hg38 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$C'" > knownCanonical/$C.known.bed
    done

    ls knownCanonical/*.known.bed | while read F
    do
      if [ -s $F ]; then
         echo $F | sed -e 's#knownCanonical/##; s/.known.bed//'
      fi
    done | while read C
    do
	echo "date"
	echo "mafGene -geneBeds=knownCanonical/$C.known.bed -noTrans $db $mz knownGene order.list stdout | \
	    gzip -c > protNuc/$C.protNuc.fa.gz"
	echo "mafGene -geneBeds=knownCanonical/$C.known.bed $db $mz knownGene order.list stdout | \
	    gzip -c > protAA/$C.protAA.fa.gz"
    done > $gp.$mz.prot.jobs

    time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1
    # 267m58.813s

    rm *.known.bed
    export mz=multiz30way
    export gp=knownCanonical
    export db=hg38
    zcat protAA/c*.gz | gzip -c > $gp.$mz.protAA.fa.gz &
    zcat protNuc/c*.gz | gzip -c > $gp.$mz.protNuc.fa.gz &
    # about 6 minutes

    ### knownCanonical broken up by exon
    cd /hive/data/genomes/hg38/bed/multiz100way/pal
    export mz=multiz100way
    export gp=knownCanonical
    export db=hg38
    mkdir exonAA exonNuc knownCanonical

    time cut -f1 ../../../chrom.sizes | while read C
    do
        echo $C 1>&2
	hgsql hg38 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$C'" > knownCanonical/$C.known.bed
    done
    #   real    0m15.897s

    ls knownCanonical/*.known.bed | while read F
    do
      if [ -s $F ]; then
         echo $F | sed -e 's#knownCanonical/##; s/.known.bed//'
      fi
    done | while read C
    do
	echo "date"
	echo "mafGene -geneBeds=knownCanonical/$C.known.bed -exons -noTrans $db $mz knownGene order.list stdout | \
	    gzip -c > exonNuc/$C.exonNuc.fa.gz"
	echo "mafGene -geneBeds=knownCanonical/$C.known.bed -exons $db $mz knownGene order.list stdout | \
	    gzip -c > exonAA/$C.exonAA.fa.gz"
    done > $gp.$mz.jobs

    time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1
    # 267m58.813s

    rm *.known.bed
    export mz=multiz30way
    export gp=knownCanonical
    export db=hg38
    zcat exonAA/c*.gz | gzip -c > $gp.$mz.exonAA.fa.gz &
    zcat exonNuc/c*.gz | gzip -c > $gp.$mz.exonNuc.fa.gz &
    # about 6 minutes

    rm -rf exonAA exonNuc

    export mz=multiz100way
    export gp=knownCanonical
    export db=hg38
    export pd=/usr/local/apache/htdocs-hgdownload/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
    ln -s `pwd`/$gp.$mz.protAA.fa.gz $pd/$gp.protAA.fa.gz
    ln -s `pwd`/$gp.$mz.protNuc.fa.gz $pd/$gp.protNuc.fa.gz
    cd  $pd
    md5sum *.fa.gz > md5sum.txt

    rm -rf exonAA exonNuc

    export mz=multiz30way
    export gp=knownCanonical
    export db=hg38
    export pd=/usr/local/apache/htdocs-hgdownload/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

    # knownGene
    export mz=multiz30way
    export gp=knownGene
    export db=hg38
    export I=0
    export D=0
    mkdir exonAA exonNuc
    for C in `sort -nk2 ../../../chrom.sizes | cut -f1`
    do
        I=`echo $I | awk '{print $1+1}'`
        D=`echo $D | awk '{print $1+1}'`
        dNum=`echo $D | awk '{printf "%03d", int($1/300)}'`
        mkdir -p exonNuc/${dNum} > /dev/null
        mkdir -p exonAA/${dNum} > /dev/null
	echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/${dNum}/$C.exonNuc.fa.gz &"
	echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/${dNum}/$C.exonAA.fa.gz &"
        if [ $I -gt 16 ]; then
            echo "date"
            echo "wait"
            I=0
        fi
    done > $gp.jobs
    echo "date" >> $gp.jobs
    echo "wait" >> $gp.jobs

    time (sh -x ./$gp.jobs) > $gp.jobs.log 2>&1
    # real    79m18.323s

    export mz=multiz30way
    export gp=knownGene
    time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonAA.fa.gz
    # real    1m28.841s

    time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \
     | gzip -c > $gp.$mz.exonNuc.fa.gz
    #   real    3m56.370s

    # -rw-rw-r-- 1 397928833 Nov  6 18:44 knownGene.multiz30way.exonAA.fa.gz
    # -rw-rw-r-- 1 580377720 Nov  6 18:49 knownGene.multiz30way.exonNuc.fa.gz

    export mz=multiz30way
    export gp=knownGene
    export db=hg38
    export pd=/usr/local/apache/htdocs-hgdownload/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
    ln -s `pwd`/md5sum.txt $pd/

    cd  $pd
    md5sum *.fa.gz > md5sum.txt

    rm -rf exonAA exonNuc

#############################################################################
# wiki page for 30-way (DONE - 2017-11-06 - Hiram)
    mkdir /hive/users/hiram/bigWays/hg38.30way
    cd /hive/users/hiram/bigWays
    echo "hg38" > hg38.30way/ordered.list
    awk '{print $1}' /hive/data/genomes/hg38/bed/multiz30way/30way.distances.txt \
       >> hg38.30way/ordered.list

    # sizeStats.sh catches up the cached measurements required for data
    # in the tables.  They are usually already mostly done, only new
    # assemblies will have updates.
    ./sizeStats.sh hg38.30way/ordered.list
    # dbDb.sh constructs hg38.30way/XenTro9_30-way_conservation_alignment.html
    # may need to add new assembly references to srcReference.list and
    # urlReference.list
    ./dbDb.sh hg38 30way
    # sizeStats.pl constructs hg38.30way/XenTro9_30-way_Genome_size_statistics.html
    # this requires entries in coverage.list for new sequences
    ./sizeStats.pl hg38 30way

    # defCheck.pl constructs XenTro9_30-way_conservation_lastz_parameters.html
    ./defCheck.pl hg38 30way

    # this constructs the html pages in hg38.30way/:
# -rw-rw-r-- 1 6247 May  2 17:07 XenTro9_30-way_conservation_alignment.html
# -rw-rw-r-- 1 8430 May  2 17:09 XenTro9_30-way_Genome_size_statistics.html
# -rw-rw-r-- 1 5033 May  2 17:10 XenTro9_30-way_conservation_lastz_parameters.html

    # add those pages to the genomewiki.  Their page names are the
    # names of the .html files without the .html:
#  XenTro9_30-way_conservation_alignment
#  XenTro9_30-way_Genome_size_statistics
#  XenTro9_30-way_conservation_lastz_parameters

    # when you view the first one you enter, it will have links to the
    # missing two.

############################################################################
# pushQ readmine (DONE - 2017-11-07 - Hiram)

  cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg38
  find -L `pwd`/multiz30way `pwd`/phastCons30way `pwd`/phyloP30way \
	/gbdb/hg38/multiz30way -type f \
    > /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList
  wc -l /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList
# 1450 /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList

  cd /hive/data/genomes/hg38/bed/multiz30way/downloads
  hgsql -e 'show tables;' hg38 | grep 30way \
	| sed -e 's/^/hg38./;' > redmine.20216.table.list

############################################################################
# SSREV model phyloFit for 30-way (DONE - 2021-10-26 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/multiz30way/4dSSREV
    cd /hive/data/genomes/hg38/bed/multiz30way/4dSSREV

    # re-use the mfa file from the first 4d calculation:

    /hive/data/genomes/hg38/bed/multiz30way/4dSSREV
    ln -s ../4d/4d.all.mfa .
    ln -s ../4d/treeCommas.nh .

    # use phyloFit to create tree model (output is phyloFit.mod)
    time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/phyloFit \
	    --EM --precision MED --msa-format FASTA --subst-mod SSREV \
		--tree tree-commas.nh 4d.all.mfa
    #   real    4m51.712s

    mv phyloFit.mod all.SSREV.mod

    grep TREE all.SSREV.mod
# ((((((((((((hg38:0.0101822,panTro5:0.0025629):0.00183633,
# panPan2:0.00255247):0.00567321,gorGor5:0.00857341):0.00933067,
# ponAbe2:0.0183779):0.00329369,nomLeu3:0.022487):0.0111263,
# (((((rheMac8:0.00266035,(macFas5:0.0021818,
# macNem1:0.00424292):0.00180259):0.00606931,cerAty1:0.00671163):0.00176629,
# papAnu3:0.00691103):0.00179762,(chlSab2:0.0163484,
# manLeu1:0.00699997):0.0016666):0.00933071,((nasLar1:0.00767798,
# colAng1:0.0163858):0.00172077,(rhiRox1:0.00212606,
# rhiBie1:0.00222663):0.00577192):0.0104159):0.0214006):0.020624,
# (((calJac3:0.0358326,saiBol1:0.0323928):0.00177708,
# cebCap1:0.0283119):0.00205848,aotNan1:0.0232272):0.0378502):0.060658,
# tarSyr2:0.142136):0.0112106,(((micMur3:0.056364,
# proCoq1:0.0388123):0.00536667,(eulMac1:0.00218455,
# eulFla1:0.00228788):0.0410379):0.0371557,
# otoGar3:0.132659):0.0335083):0.0179418,mm10:0.344669):0.0240895,
# canFam3:0.163925):0.0880641,dasNov3:0.0880641);

    # compare these calculated lengths to what was calculated before:

    grep TREE ../4d/all.mod | sed -e 's/TREE: //;' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep hg38 \
          | sed -e "s/hg38.//;"  | sort > original.dists

    grep TREE all.SSREV.mod | sed -e 's/TREE: //;' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep hg38 \
          | sed -e "s/hg38.//;"  | sort > SSREV.dists

    # printing out the 'original', the 'new' the 'difference' and
    #    percent difference/delta
    join original.dists SSREV.dists | awk '{
  printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%8.6f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }'       | sort -k4n
#       panTro5 0.012747        0.012745        0.000002        0.015692
#       panPan2 0.014424        0.014571        -0.000147       -1.008853
#       gorGor5 0.026112        0.026265        -0.000153       -0.582524
#       ponAbe2 0.045247        0.045400        -0.000153       -0.337004
#       nomLeu3 0.052648        0.052803        -0.000155       -0.293544
#       manLeu1 0.080673        0.080840        -0.000167       -0.206581
#       papAnu3 0.080660        0.080882        -0.000222       -0.274474
#       rhiRox1 0.081014        0.081157        -0.000143       -0.176202
#       rhiBie1 0.081111        0.081257        -0.000146       -0.179677
#       cerAty1 0.082107        0.082449        -0.000342       -0.414802
#       nasLar1 0.082467        0.082658        -0.000191       -0.231073
#       rheMac8 0.084120        0.084467        -0.000347       -0.410811
#       macFas5 0.085357        0.085791        -0.000434       -0.505881
#       macNem1 0.087416        0.087852        -0.000436       -0.496289
#       chlSab2 0.090031        0.090189        -0.000158       -0.175188
#       colAng1 0.091177        0.091365        -0.000188       -0.205768
#       aotNan1 0.122992        0.123144        -0.000152       -0.123433
#       cebCap1 0.130086        0.130287        -0.000201       -0.154275
#       saiBol1 0.135917        0.136145        -0.000228       -0.167469
#       calJac3 0.139357        0.139585        -0.000228       -0.163341
#       eulMac1 0.247615        0.247821        -0.000206       -0.083125
#       eulFla1 0.247716        0.247925        -0.000209       -0.084300
#       proCoq1 0.248499        0.248778        -0.000279       -0.112148
#       tarSyr2 0.264791        0.264860        -0.000069       -0.026051
#       micMur3 0.266045        0.266330        -0.000285       -0.107010
#       otoGar3 0.300022        0.300102        -0.000080       -0.026658
#       canFam3 0.339655        0.339891        -0.000236       -0.069434
#       dasNov3 0.351919        0.352094        -0.000175       -0.049703
#       mm10    0.496188        0.496546        -0.000358       -0.072098

#########################################################################
# phyloP SSREV for 30-way (DONE - 2021-10-26 - Hiram)
#
    # re-use the split SS files from before
    # split SS files into 1M chunks, this business needs smaller files
    #   to complete

    mkdir  /hive/data/genomes/hg38/bed/multiz30way/phyloP.SSREV
    cd  /hive/data/genomes/hg38/bed/multiz30way/phyloP.SSREV

    # run phyloP with score=LRT

    mkdir run.phyloP
    cd run.phyloP
    # Adjust model file base composition background and rate matrix to be
    # representative of the chromosomes in play
    grep BACK ../../4dSSREV/all.SSREV.mod
    #   BACKGROUND: 0.207173 0.328301 0.237184 0.227343

    grep BACKGROUND ../../4dSSREV/all.SSREV.mod \
       | awk '{printf "%0.3f\n", $3 + $4}'
    #	0.565
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../4dSSREV/all.SSREV.mod 0.565 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #	BACKGROUND: 0.217500 0.282500 0.282500 0.217500

    printf '#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set f = $1
set ssFile = $1:t
set out = $2
set cName = $f:h
set n = $f:r:e
set grp = $cwd:t
set prevCons = /hive/data/genomes/hg38/bed/multiz30way/consPhyloP
set cons = /hive/data/genomes/hg38/bed/multiz30way/phyloP.SSREV
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "$prevCons/ss/$cName/$ssFile"
set useGrp = "$grp.mod"
/bin/ln -s $cons/run.phyloP/$grp.mod $tmp
pushd $tmp > /dev/null
$PHASTBIN/phyloP --method LRT --mode CONACC --wig-scores --chrom $cName \
    -i SS $useGrp $ssSrc.ss > $ssFile.wigFix
popd > /dev/null
/bin/mkdir -p $out:h
sleep 4
/bin/touch $out:h
/bin/mv $tmp/$ssFile.wigFix $out
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp
' > doPhyloP.csh

    chmod +x doPhyloP.csh

    # re-use list of chunks
    ln -s ../../consPhyloP/run.phyloP/ss.list .

    # make sure the list looks good
    wc -l ss.list
    #	3308 ss.list

    # Create template file
    #	file1 == $chr/$chunk/file name without .ss suffix
    printf '#LOOP
../run.phyloP/doPhyloP.csh $(path1) {check out line+ wigFix/$(dir1)/$(file1).wigFix}
#ENDLOOP
' > template

    ######################   Running all species  #######################
    # setup run for all species
    mkdir /hive/data/genomes/hg38/bed/multiz30way/phyloP.SSREV/all
    cd /hive/data/genomes/hg38/bed/multiz30way/phyloP.SSREV/all
    rm -fr wigFix
    mkdir wigFix

    gensub2 ../run.phyloP/ss.list single ../run.phyloP/template jobList
    # beware overloading the cluster with these quick and high I/O jobs
    para -ram=32g create jobList
    para try ... check ...
    para push
    para time > run.time

# Completed: 3308 of 3308 jobs
# CPU time in finished jobs:     682943s   11382.39m   189.71h    7.90d  0.022 y
# IO & Wait Time:                 22200s     369.99m     6.17h    0.26d  0.001 y
# Average job time:                 213s       3.55m     0.06h    0.00d
# Longest finished job:             405s       6.75m     0.11h    0.00d
# Submission to last job:          3562s      59.37m     0.99h    0.04d


    mkdir downloads
    time for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'`
do
    echo "working: $D" 1>&2
    find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \
	| sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \
        | gzip -c > downloads/${D}.phyloP30way.wigFix.gz
done
    #   real    31m52.226s

    du -hsc downloads
    #   4.2G    downloads

    # check integrity of data with wigToBigWig
    time (zcat downloads/*.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/hg38/chrom.sizes \
	phyloP30way.bw) > bigWig.log 2>&1
XXX - working - Tue Oct 26 12:43:42 PDT 2021


    egrep "real|VmPeak" bigWig.log
    # pid=78042: VmPeak:    33938800 kB
    #  real    34m4.165s

    bigWigInfo phyloP30way.bw  | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 5,762,987,667
# primaryIndexSize: 93,404,704
# zoomLevels: 10
# chromCount: 355
# basesCovered: 2,955,660,581
# mean: 0.100336
# min: -20.000000
# max: 1.226000
# std: 0.723021

    #	encode those files into wiggle data
    time (zcat downloads/*.wigFix.gz \
	| wigEncode stdin phyloPSSREV30way.wig phyloPSSREV30way.wib)

# Converted stdin, upper limit 1.23, lower limit -20.00
# real    13m31.412s
# -rw-rw-r--   1 2955660581 Oct 27 12:23 phyloPSSREV30way.wib
# -rw-rw-r--   1  318831430 Oct 27 12:23 phyloPSSREV30way.wig

    du -hsc *.wi?
    # 2.8G    phyloP30way.wib
    # 305M    phyloP30way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloPSSREV30way.wib /gbdb/hg38/multiz30way/phyloPSSREV30way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz30way hg38 \
	phyloPSSREV30way phyloPSSREV30way.wig
    # real    0m18.359s

    # use to set trackDb.ra entries for wiggle min and max
    # and verify table is loaded correctly

    wigTableStats.sh hg38 phyloPSSREV30way
# db.table                min   max     mean       count     sumData
# hg38.phyloPSSREV30way   -20 1.226 0.100336 2955660581 2.96558e+08
#       stdDev viewLimits
#      0.723021 viewLimits=-3.51477:1.226
# hg38.phyloP30way  -20 1.312 0.0978331 2955660581 2.89162e+08
#     0.727453 viewLimits=-3.53943:1.312

    #	that range is: 20+1.226= 21.226 for hBinSize=0.021226

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram \
	-hBinSize=0.021226 -hBinCount=1000 -hMinVal=-20 -verbose=2 \
	    -db=hg38 phyloPSSREV30way > histogram.data 2>&1
    #   real    1m54.621s

    # xaxis range:
    grep -v chrom histogram.data | grep "^[0-9]" | ave -col=2 stdin \
	| sed -e 's/^/# /;'
# Q1 -10.947100
# median -6.892945
# Q3 -2.838780
# average -6.908920
# min -20.000000
# max 1.204770
# count 764
# total -5278.414760
# standard deviation 4.715614

# Q1 -10.953050
# median -6.861155
# Q3 -2.769245
# average -6.875971
# min -20.000000
# max 1.312000
# count 768
# total -5280.745380
# standard deviation 4.757034

    # find out the range for the 2:5 graph
    grep -v chrom histogram.data | grep "^[0-9]" | ave -col=5 stdin \
      | sed -e 's/^/# /;'
# Q1 0.000000
# median 0.000001
# Q3 0.000126
# average 0.001309
# min 0.000000
# max 0.022808
# count 764
# total 0.999990
# standard deviation 0.003612

# Q1 0.000000
# median 0.000001
# Q3 0.000140
# average 0.001302
# min 0.000000
# max 0.023556
# count 768
# total 0.999975
# standard deviation 0.003490

    #	create plot of histogram:
    printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \

    printf 'set terminal pngcairo size 900,400 background "#000000" \\
font "/usr/share/fonts/default/Type1/n022004l.pfb"
set size 1.4, 0.8
set key left box
set grid noxtics
set grid ytics
set title " Human hg38 Histogram phyloPSSREV30way track"
set xlabel " phyloPSSREV30way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set xrange [-5:1.5]
set yrange [0:0.04]

plot "histogram.data" using 2:5 title " RelFreq" with impulses, \
        "histogram.data" using 2:7 axes x1y2 title " CRF" with lines
' | gnuplot > histo.png

    # verify it looks sane
    display histo.png &

#############################################################################
# sequence logo
    mkdir /hive/data/genomes/hg38/bed/multiz30way/logo
    cd /hive/data/genomes/hg38/bed/multiz30way/logo
    mkdir wigs bw 

    ls ../maf/* | awk '{printf "./makeWig.sh %s ../consPhyloP/all/phyloP30way.bw ../../../chrom.sizes\n", $1}' > jobs

    cat << '_EOF_' > makeWig.sh
maf=$1
scale=$2
chromSizes=$3
outRoot=`basename $1 .maf`
mafCounts -scale=$scale $maf wigs/$outRoot
for i in A C G T
do
    wigToBigWig -keepAllChromosomes -fixedSummaries wigs/$outRoot.$i.wig $chromSizes bw/$outRoot.$i.bw
done
'_EOF_'

    chmod +x makeWig.sh

    ssh ku "cd /hive/data/genomes/hg38/bed/multiz30way/logo; para make jobs"

    for i in A C G T
    do
        bigWigCat multiz30Logo.$i.bw bw/*.$i.bw &
    done

    wait

    for i in A C G T
    do
        ln -s `pwd`/multiz30Logo.$i.bw /gbdb/hg38/multiz30way/
    done

