#############################################################################
## 17-Way Multiz (DONE - 2015-02-26 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/hg38/bed/multiz17way
    cd /hive/data/genomes/hg38/bed/multiz17way

    # from the 63-way in the source tree, select out the 7 used here:
    /cluster/bin/phast/tree_doctor \
        --prune-all-but hg38,panTro4,panPan1,gorGor3,ponAbe2,nomLeu3,rheMac3,macFas5,papAnu2,chlSab2,nasLar1,rhiRox1,calJac3,saiBol1,tarSyr2,micMur1,otoGar3 \
        /cluster/home/hiram/kent/src/hg/utils/phyloTrees/183way.nh \
          > hg38.17way.nh

    #	what that looks like:
 ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.17way.nh | sed -e 's/^/# /;'
# (((((((((hg38:0.00655,
#         panTro4:0.00684):0.00122,
#        panPan1:0.00784):0.003,
#       gorGor3:0.008964):0.009693,
#      ponAbe2:0.01894):0.003471,
#     nomLeu3:0.02227):0.01204,
#    ((((rheMac3:0.004991,
#       macFas5:0.004991):0.003,
#      papAnu2:0.008042):0.01061,
#     chlSab2:0.027):0.005,
#    (nasLar1:0.0015,
#    rhiRox1:0.001500):0.018000):0.020000):0.021830,
#   (calJac3:0.03,
#   saiBol1:0.010350):0.019650):0.052090,
#  tarSyr2:0.1114):0.02052,
# (micMur1:0.0856,
# otoGar3:0.1194):0.02052);

    # extract species list from that .nh file
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
        hg38.17way.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/-nosed/_nosed/; s/-eating/_eating/;' > db.to.name.txt

    # construct a common name .nh file:
    /cluster/bin/phast/tree_doctor --rename \
    "`cat db.to.name.txt`" hg38.17way.nh | sed -e 's/00*)/)/g; s/00*,/,/g' \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > hg38.17way.commonNames.nh
    cat hg38.17way.commonNames.nh | sed -e 's/^/# /;'
# (((((((((Human:0.00655,
#         Chimp:0.00684):0.00122,
#        Bonobo:0.00784):0.001,
#       Gorilla:0.008964):0.009693,
#      Orangutan:0.01894):0.003471,
#     Gibbon:0.02227):0.01204,
#    ((((Rhesus:0.004991,
#       Crab_eating_macaque:0.004991):0.003,
#      Baboon:0.008042):0.01961,
#     Green_monkey:0.027):0.005,
#    (Proboscis_monkey:0.02,
#    Golden_snub_nosed_monkey:0.02):0.01):0.005):0.02183,
#   (Marmoset:0.05,
#   Squirrel_monkey:0.01035):0.01965):0.05209,
#  Tarsier:0.1114):0.02052,
# (Mouse_lemur:0.0856,
# Bushbaby:0.1194):0.02052);

#	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_17way.png
    grep TREE 4d/all.mod | awk '{print $NF}' \
       | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
	| $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
	    > hg38.17way.scientificNames.nh

    ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.17way.nh > t.nh
    ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \
       | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
          > hg38.17way.scientificNames.nh
    rm -f t.nh
    cat hg38.17way.scientificNames.nh | sed -e 's/^/# /;'
# (((((((((Homo_sapiens:0.00655,
#         Pan_troglodytes:0.00684):0.00122,
#        Pan_paniscus:0.00784):0.001,
#       Gorilla_gorilla_gorilla:0.008964):0.009693,
#      Pongo_pygmaeus_abelii:0.01894):0.003471,
#     Nomascus_leucogenys:0.02227):0.01204,
#    ((((Macaca_mulatta:0.004991,
#       Macaca_fascicularis:0.004991):0.003,
#      Papio_anubis:0.008042):0.01961,
#     Chlorocebus_sabaeus:0.027):0.005,
#    (Nasalis_larvatus:0.02,
#    Rhinopithecus_roxellana:0.02):0.01):0.005):0.02183,
#   (Callithrix_jacchus:0.05,
#   Saimiri_boliviensis:0.01035):0.01965):0.05209,
#  Tarsius_syrichta:0.1114):0.02052,
# (Microcebus_murinus:0.0856,
# Otolemur_garnettii:0.1194):0.02052);

    /cluster/bin/phast/all_dists hg38.17way.nh | grep hg38 \
        | sed -e "s/hg38.//" | sort -k2n > 17way.distances.txt
    #	Use this output to create the table below
    cat 17way.distances.txt | sed -e 's/^/# /;'
# panTro4       0.013390
# panPan1       0.015610
# gorGor3       0.017734
# ponAbe2       0.037403
# nomLeu3       0.044204
# nasLar1       0.068974
# rhiRox1       0.068974
# chlSab2       0.070974
# macFas5       0.071575
# rheMac3       0.071575
# papAnu2       0.071626
# saiBol1       0.085804
# calJac3       0.125454
# tarSyr2       0.219294
# micMur1       0.234534
# otoGar3       0.268334

    cat << '_EOF_' > sizeStats.pl
#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<17way.distances.txt") or
        die "can not read 17way.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);
'_EOF_'
    # << happy emacs
    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 (% 93.112) (% 95.664) - Chimp panTro4
# 02  0.0156 (% 92.929) (% 97.795) - Bonobo panPan1
# 03  0.0177 (% 88.005) (% 91.695) - Gorilla gorGor3
# 04  0.0374 (% 89.187) (% 89.656) - Orangutan ponAbe2
# 05  0.0442 (% 86.379) (% 90.470) - Gibbon nomLeu3
# 06  0.0690 (% 74.541) (% 89.972) - Proboscis monkey nasLar1
# 07  0.0690 (% 74.547) (% 71.639) - Golden snub-nosed monkey rhiRox1
# 08  0.0710 (% 84.393) (% 88.264) - Green monkey chlSab2
# 09  0.0716 (% 85.675) (% 87.749) - Crab-eating macaque macFas5
# 10  0.0716 (% 79.729) (% 86.715) - Rhesus rheMac3
# 11  0.0716 (% 84.179) (% 84.502) - Baboon papAnu2
# 12  0.0858 (% 70.565) (% 81.466) - Squirrel monkey saiBol1
# 13  0.1255 (% 71.709) (% 76.757) - Marmoset calJac3
# 14  0.2193 (% 56.022) (% 52.305) - Tarsier tarSyr2
# 15  0.2345 (% 42.653) (% 00.000) - Mouse lemur micMur1
# 16  0.2683 (% 49.485) (% 60.561) - Bushbaby otoGar3

# None of this concern for distances matters in building the first step, the
# maf files.

    # create species list and stripped down tree for autoMZ
    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	hg38.17way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh

    sed 's/[()]//g; s/,/ /g' tree.nh > species.list
    #   hg38 panTro4 rheMac3 mm10 rn5 canFam3 monDom5

    #	bash shell syntax here ...
    cd /hive/data/genomes/hg38/bed/multiz17way
    export H=/hive/data/genomes/hg38/bed
    mkdir mafLinks

    # good assemblies can use syntenic net:
    #  panTro4 nomLeu3 ponAbe2 chlSab2 macFas5 rheMac3 papAnu2 calJac3
    for G in panTro4 nomLeu3 ponAbe2 chlSab2 macFas5 rheMac3 papAnu2 calJac3
    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:
    #  saiBol1 panPan1 gorGor3 nasLar1 rhiRox1 micMur1 otoGar3 tarSyr2
    for G in  saiBol1 panPan1 gorGor3 nasLar1 rhiRox1 micMur1 otoGar3 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 -ogrtL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;'
#  1277455681 Jan 28  2014 mafLinks/rheMac3/hg38.rheMac3.synNet.maf.gz
#  1463969868 May 27  2014 mafLinks/panTro4/hg38.panTro4.synNet.maf.gz
#  1375738965 Jul 11 21:00 mafLinks/chlSab2/hg38.chlSab2.synNet.maf.gz
#  1316871557 Sep  2 15:26 mafLinks/ponAbe2/hg38.ponAbe2.synNet.maf.gz
#  1545631156 Dec 12 10:57 mafLinks/panPan1/hg38.panPan1.rbest.maf.gz
#  1333531476 Dec 12 21:40 mafLinks/nomLeu3/hg38.nomLeu3.synNet.maf.gz
#  1109719031 Dec 13 15:48 mafLinks/tarSyr2/hg38.tarSyr2.rbest.maf.gz
#  1145428744 Dec 13 16:15 mafLinks/rhiRox1/hg38.rhiRox1.rbest.maf.gz
#  1479839247 Dec 13 16:38 mafLinks/papAnu2/hg38.papAnu2.synNet.maf.gz
#  1275300135 Dec 13 17:50 mafLinks/calJac3/hg38.calJac3.synNet.maf.gz
#  1003860248 Dec 13 20:23 mafLinks/otoGar3/hg38.otoGar3.rbest.maf.gz
#  1403994424 Dec 14 03:03 mafLinks/macFas5/hg38.macFas5.synNet.maf.gz
#  1194459441 Dec 14 23:26 mafLinks/saiBol1/hg38.saiBol1.rbest.maf.gz
#  1153387036 Dec 15 19:26 mafLinks/gorGor3/hg38.gorGor3.rbest.maf.gz
#  1145326563 Dec 15 22:26 mafLinks/nasLar1/hg38.nasLar1.rbest.maf.gz
#   838465015 Dec 19 21:48 mafLinks/micMur1/hg38.micMur1.rbest.maf.gz

    # split the maf files into a set of hashed named files
    # this hash named split keeps the same chr/contig names in the same
    # named hash file.
    mkdir /hive/data/genomes/hg38/bed/multiz17way/mafSplit
    cd /hive/data/genomes/hg38/bed/multiz17way/mafSplit
    time for D in `sed -e "s/hg38 //" ../species.list`
do
    echo "${D}"
    mkdir $D
    cd $D
    echo "mafSplit -byTarget -useHashedName=8 /dev/null . ../../mafLinks/${D}/*.maf.gz"
    mafSplit -byTarget -useHashedName=8 /dev/null . \
	../../mafLinks/${D}/*.maf.gz
    cd ..
done
    # real    21m42.070s

    # XXX will have to do this different next time.  These cluster jobs
    # ran too long to be practical for larger alignments.

    # construct a list of all possible maf file names.
    # they do not all exist in each of the species directories
    find . -type f | wc -l
    # 1488
    find . -type f | grep ".maf$" | xargs -L 1 basename | sort -u > maf.list
    wc -l maf.list
    # 120 maf.list

    mkdir /hive/data/genomes/hg38/bed/multiz17way/splitRun
    cd /hive/data/genomes/hg38/bed/multiz17way/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/multiz17way/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
'_EOF_'
# << happy emacs
    chmod +x autoMultiz.csh

    cat  << '_EOF_' > template
#LOOP
./autoMultiz.csh $(file1) {check out line+ /hive/data/genomes/hg38/bed/multiz17way/splitRun/maf/$(root1).maf}
#ENDLOOP
'_EOF_'
# << happy emacs

    ln -s ../../mafSplit/maf.list maf.list
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz17way/splitRun/run
    gensub2 maf.list single template stdout > jobList
    para create jobList
# Completed: 120 of 120 jobs
# CPU time in finished jobs:    1378875s   22981.25m   383.02h   15.96d  0.044 y
# IO & Wait Time:                  5677s      94.62m     1.58h    0.07d  0.000 y
# Average job time:               11538s     192.30m     3.20h    0.13d
# Longest finished job:          120451s    2007.52m    33.46h    1.39d
# Submission to last job:        120463s    2007.72m    33.46h    1.39d

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    cd /hive/data/genomes/hg38/bed/multiz17way
    head -1 splitRun/maf/017.maf > multiz17way.maf
    time for F in splitRun/maf/*.maf
do
    echo "${F}" 1>&2
    egrep -v "^#" ${F}
done >> multiz17way.maf
   # real    1m48.859s

    tail -1 splitRun/maf/017.maf >> multiz17way.maf
# with the correct rhiRox1 sequence:
# -rw-rw-r--  1 55747928868 Feb 26 16:00 multiz17way.maf
# when rhiRox1 was identical to nasLar1:
# -rw-rw-r-- 1 15635828403 Jun  3 11:49 multiz17way.maf

    # Load into database
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz17way
    mkdir /gbdb/hg38/multiz17way
    ln -s `pwd`/multiz17way.maf /gbdb/hg38/multiz17way
    cd /dev/shm
    time hgLoadMaf hg38 multiz17way
# with the correct rhiRox1 sequence:
    # Loaded 18692177 mafs in 1 files from /gbdb/hg38/multiz17way
    # real    11m47.253s

# when rhiRox1 was identical to nasLar1:
    # Loaded 17829760 mafs in 1 files from /gbdb/hg38/multiz17way
    #  real    11m31.641s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 hg38 multiz17waySummary \
	/gbdb/hg38/multiz17way/multiz17way.maf
# with the correct rhiRox1 sequence:
    # Created 2291702 summary blocks from 220323246 components and 18692177
    #    mafs from /gbdb/hg38/multiz17way/multiz17way.maf
    # real    21m44.820s
# when rhiRox1 was identical to nasLar1:
    # Created 2347550 summary blocks from 208312034 components and 17829760
    # mafs from /gbdb/hg38/multiz17way/multiz17way.maf
    #  real    21m5.003s

    wc -l multiz17way*.tab
# with the correct rhiRox1 sequence:
    # 18692177 multiz17way.tab
    #  2291702 multiz17waySummary.tab
# when rhiRox1 was identical to nasLar1:
    #   17829760 multiz17way.tab
    #    2347550 multiz17waySummary.tab

    rm multiz17way*.tab

##############################################################################
# GAP ANNOTATE MULTIZ7WAY MAF AND LOAD TABLES (DONE - 2015-02-26 - 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.  Need to split of the maf file into individual
    #   maf files
    mkdir -p /hive/data/genomes/hg38/bed/multiz17way/anno/mafSplit
    cd /hive/data/genomes/hg38/bed/multiz17way/anno/mafSplit

    time mafSplit -outDirDepth=1 -byTarget -useFullSequenceName \
        /dev/null . ../../multiz17way.maf

    find . -type f | wc -l
    #   358

    # check for N.bed files everywhere:
    cd /hive/data/genomes/hg38/bed/multiz17way/anno
    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
done

    cd /hive/data/genomes/hg38/bed/multiz17way/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

    screen -S hg38      # use a screen to control this longish job
    ssh ku
    cd /hive/data/genomes/hg38/bed/multiz17way/anno
    mkdir result
    for D in `ls mafSplit`
do
    echo mkdir result/${D}
    mkdir result/${D}
done
    cat << '_EOF_' > template
#LOOP
mafAddIRows -nBeds=nBeds mafSplit/$(path1) /hive/data/genomes/hg38/hg38.2bit {check out exists+ result/$(path1)}
#ENDLOOP
'_EOF_'
    # << happy emacs

    find ./mafSplit -type f | sed -e 's#^./mafSplit/##' > maf.list
    gensub2 maf.list single template jobList
    # limit jobs on a node with the ram=32g requirement because they go fast
    para create jobList
    para try ... check ... push ...
    # don't run too many at once, these go very fast
    para -maxJob=20 push
# Completed: 358 of 358 jobs
# CPU time in finished jobs:       1974s      32.90m     0.55h    0.02d  0.000 y
# IO & Wait Time:                   933s      15.55m     0.26h    0.01d  0.000 y
# Average job time:                   8s       0.14m     0.00h    0.00d
# Longest finished job:             133s       2.22m     0.04h    0.00d
# Submission to last job:           162s       2.70m     0.04h    0.00d

    # verify all result files have some content, look for 0 size files:
    find ./result -type f -size 0
    # should see none
    # or in this manner:
    find ./result -type f | xargs ls -og | sort -k3nr | tail
# -rw-rw-r-- 1       9045 Feb 26 22:05 ./result/9/chrUn_KI270581v1.maf
# -rw-rw-r-- 1       7236 Feb 26 22:05 ./result/1/chrUn_KI270528v1.maf
# -rw-rw-r-- 1       5903 Feb 26 22:05 ./result/7/chrUn_KI270330v1.maf
# -rw-rw-r-- 1       1268 Feb 26 22:05 ./result/6/chrUn_KI270583v1.maf

    # combine into one file  (the 1>&2 redirect sends the echo to stderr)
    head -q -n 1 result/0/chr8.maf > hg38.17way.maf
    find ./result -type f | while read F
do
    echo "${F}" 1>&2
    grep -h -v "^#" ${F}
done >> hg38.17way.maf

    #	these maf files do not have the end marker, this does nothing:
    #	tail -q -n 1 result/0/chr8.maf >> hg38.17way.maf
    # How about an official end marker:
    echo "##eof maf" >> hg38.17way.maf
    ls -og
# with the correct rhiRox1 sequence:
# -rw-rw-r--  1 67644767226 Feb 26 22:15 hg38.17way.maf
# when rhiRox1 was identical to nasLar1:
# -rw-rw-r-- 1 65649174703 Dec 22 14:32 hg38.17way.maf

    du -hsc hg38.17way.maf
    # 63G     hg38.17way.maf

    # construct symlinks to get the individual maf files into gbdb:
    rm /gbdb/hg38/multiz17way/multiz17way.maf   # remove previous results
    ln -s `pwd`/hg38.17way.maf /gbdb/hg38/multiz17way/multiz17way.maf

    # Load into database
    cd /dev/shm
    time hgLoadMaf -pathPrefix=/gbdb/hg38/multiz17way \
        hg38 multiz17way
# with the correct rhiRox1 sequence:
    # Loaded 18733383 mafs in 1 files from /gbdb/hg38/multiz17way
    # real    13m46.128s
# when rhiRox1 was identical to nasLar1:
    # Loaded 17870998 mafs in 1 files from /gbdb/hg38/multiz17way
    # real    13m28.939s

    time hgLoadMafSummary -verbose=2 -minSize=30000 \
	-mergeGap=1500 -maxSize=200000 hg38 multiz17waySummary \
        /gbdb/hg38/multiz17way/multiz17way.maf
    # with the correct rhiRox1 sequence:
    # Created 2291702 summary blocks from 220323246 components and
    #    18733383 mafs from /gbdb/hg38/multiz17way/multiz17way.maf
    # real    25m13.821s

    # when rhiRox1 was identical to nasLar1:
# Created 2347550 summary blocks from 208312034 components and 17870998 mafs
# from /gbdb/hg38/multiz17way/multiz17way.maf
    # real    23m17.086s

    # with the correct rhiRox1 sequence:
# -rw-rw-r--  1 982790471 Feb 26 22:29 multiz17way.tab
# -rw-rw-r--  1 112999853 Feb 26 23:03 multiz17waySummary.tab

    # when rhiRox1 was identical to nasLar1:
# -rw-rw-r-- 1 919768167 Dec 22 14:45 multiz17way.tab
# -rw-rw-r-- 1 115753412 Dec 22 15:29 multiz17waySummary.tab

    wc -l multiz17way*
    #  17870998 multiz17way.tab
    #   2347550 multiz17waySummary.tab

    rm multiz17way*.tab

######################################################################
# MULTIZ7WAY MAF FRAMES (DONE - 2015-02-27 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/hg38/bed/multiz17way/frames
    cd /hive/data/genomes/hg38/bed/multiz17way/frames
#   survey all the genomes to find out what kinds of gene tracks they have
    cat << '_EOF_' > showGenes.csh
#!/bin/csh -fe
foreach db (`cat ../species.list`)
    echo -n "${db}: "
    set tables = `hgsql $db -N -e "show tables like '%Gene%'"`
    foreach table ($tables)
        if ($table == "ensGene" || $table == "refGene" || \
           $table == "mgcGenes" || $table == "knownGene" || \
           $table == "xenoRefGene" ) then
           set count = `hgsql $db -N -e "select count(*) from $table"`
            echo -n "${table}: ${count}, "
        endif
    end
    set orgName = `hgsql hgcentraltest -N -e \
            "select scientificName from dbDb where name='$db'"`
    set orgId = `hgsql hg19 -N -e \
            "select id from organism where name='$orgName'"`
    if ($orgId == "") then
        echo "Mrnas: 0"
    else
        set count = `hgsql hg19 -N -e "select count(*) from gbCdnaInfo where organism=$orgId"`
        echo "Mrnas: ${count}"
    endif
end
'_EOF_'
    # << happy emacs
    chmod +x ./showGenes.csh
    time ./showGenes.csh
# hg38: ensGene: 208239, knownGene: 104178, mgcGenes: 34081, refGene: 57615, xenoRefGene: 177355, Mrnas: 10985662
# panTro4: ensGene: 29160, refGene: 2685, xenoRefGene: 289818, Mrnas: 11222
# panPan1: xenoRefGene: 395965, Mrnas: 566
# gorGor3: ensGene: 35410, xenoRefGene: 350430, Mrnas: 1
# ponAbe2: ensGene: 29447, refGene: 3567, xenoRefGene: 298756, Mrnas: 0
# nomLeu3: xenoRefGene: 197422, Mrnas: 49
# rheMac3: refGene: 6533, xenoRefGene: 284342, Mrnas: 443910
# macFas5: refGene: 2270, xenoRefGene: 284975, Mrnas: 177455
# papAnu2: ensGene: 29028, refGene: 493, xenoRefGene: 305437, Mrnas: 146334
# chlSab2: Mrnas: 37897
# nasLar1: xenoRefGene: 324299, Mrnas: 4
# rhiRox1: xenoRefGene: 330346, Mrnas: 11
# calJac3: ensGene: 55116, refGene: 220, xenoRefGene: 313115, Mrnas: 294478
# saiBol1: xenoRefGene: 443297, Mrnas: 85
# tarSyr2: xenoRefGene: 316727, Mrnas: 8
# micMur1: ensGene: 37458, xenoRefGene: 553766, Mrnas: 59
# otoGar3: ensGene: 28565, xenoRefGene: 418798, Mrnas: 13

# real    4m47.542s

    # from that summary, use these gene sets:
    # transMap - tarSyr2 panPan1 nomLeu3 macFas5 chlSab2 saiBol1
    # knownGene - hg38
    # ensGene - panTro4 gorGor3 ponAbe2 papAnu2 calJac3 micMur1 otoGar3
    # refGene - rheMac3
    # no annotation: nasLar1 rhiRox1

    mkdir genes
    #    1. transMap genes for tarSyr2 panPan1 nomLeu3 macFas5 chlSab2
    hgsql -Ne 'select id,cds from transMapGeneUcscGenesV3' hgFixed \
       > transMapGeneUcscGenesV3.cds
    for D in tarSyr2 panPan1 nomLeu3 macFas5 chlSab2 saiBol1
do
    hgsql -Ne 'select * from transMapAlnUcscGenesV3 ' ${D} \
         | cut -f 2- \
      | mrnaToGene -ignoreUniqSuffix -quiet -insertMergeSize=0 \
       -genePredExt -keepInvalid -cdsFile=transMapGeneUcscGenesV3.cds \
        stdin stdout \
          | genePredSingleCover stdin stdout \
             | sort | gzip -2c > genes/${D}.gp.gz
    echo -n "$D: "
    genePredCheck -db=${D} genes/${D}.gp.gz
done
# tarSyr2: checked: 18728 failed: 0
# panPan1: checked: 19117 failed: 0
# nomLeu3: checked: 19201 failed: 0
# macFas5: checked: 19337 failed: 0
# chlSab2: checked: 19056 failed: 0
# saiBol1: checked: 19162 failed: 0

    #   2. knownGene: hg38
    for DB in hg38
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
    echo -n "$DB: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# hg38: checked: 21887 failed: 0

    #   3. ensGene: panTro4 gorGor3 ponAbe2 papAnu2 calJac3 micMur1 otoGar3
    for DB in panTro4 gorGor3 ponAbe2 papAnu2 calJac3 micMur1 otoGar3
do
hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from ensGene" ${DB} \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /scratch/tmp/${DB}.tmp.gz
    mv /scratch/tmp/${DB}.tmp.gz genes/$DB.gp.gz
    echo -n "$DB: "
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# panTro4: checked: 18657 failed: 0
# gorGor3: checked: 20758 failed: 0
# ponAbe2: checked: 20220 failed: 0
# papAnu2: checked: 18903 failed: 0
# calJac3: checked: 20827 failed: 0
# micMur1: checked: 28641 failed: 0
# otoGar3: checked: 19472 failed: 0

    #   4. refGene
    for DB in rheMac3
do
hgsql -N -e "select * from refGene" ${DB} | cut -f2- \
      | genePredSingleCover stdin stdout | gzip -2c \
        > /scratch/tmp/${DB}.tmp.gz
    mv /scratch/tmp/${DB}.tmp.gz genes/$DB.gp.gz
    genePredCheck -db=${DB} genes/${DB}.gp.gz
done
# checked: 5801 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/calJac3.gp.gz: 20827
# genes/chlSab2.gp.gz: 19056
# genes/gorGor3.gp.gz: 20758
# genes/hg38.gp.gz: 21887
# genes/macFas5.gp.gz: 19337
# genes/micMur1.gp.gz: 16240
# genes/nomLeu3.gp.gz: 19201
# genes/otoGar3.gp.gz: 19472
# genes/panPan1.gp.gz: 19117
# genes/panTro4.gp.gz: 18657
# genes/papAnu2.gp.gz: 18903
# genes/ponAbe2.gp.gz: 20220
# genes/rheMac3.gp.gz: 5626
# genes/saiBol1.gp.gz: 19162
# genes/tarSyr2.gp.gz: 18728

    time (cat ../anno/hg38.17way.maf \
	| nice -n +19 genePredToMafFrames hg38 stdin stdout \
           `sed -e "s/nasLar1 rhiRox1 //;" ../species.list | sed -e "s#\([a-zA-Z0-9]*\)#\1 genes/\1.gp.gz#g;"` \
		| gzip > multiz17wayFrames.bed.gz)
    #   real    13m44.958s

    # verify there are frames on everything, should be 15 species:
    zcat multiz17wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c 
       | sed -e 's/^/# /;'
#  245468 calJac3
#  225225 chlSab2
#  196578 gorGor3
#  208946 hg38
#  227955 macFas5
#  199781 micMur1
#  226624 nomLeu3
#  212700 otoGar3
#  191083 panPan1
#  200264 panTro4
#  219940 papAnu2
#  222338 ponAbe2
#   49917 rheMac3
#  211872 saiBol1
#  208117 tarSyr2

    #   load the resulting file
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz17way/frames
    time hgLoadMafFrames hg38 multiz17wayFrames multiz17wayFrames.bed.gz
    #   real    1m22.000s

    time featureBits -countGaps hg38 multiz17wayFrames
    # with the correct rhiRox1 sequence:
    # 46380672 bases of 3209286105 (1.445%) in intersection
    # real    0m42.574s
    # when rhiRox1 was identical to nasLar1:
    # 46335112 bases of 3209286105 (1.444%) in intersection
    # real    0m34.394s

    #   enable the trackDb entries:
# frames multiz17wayFrames
# irows on
    #   appears to work OK

#########################################################################
# Phylogenetic tree from 17-way (DONE - 2015-02-27 - Hiram)
    mkdir /hive/data/genomes/hg38/bed/multiz17way/4d
    cd /hive/data/genomes/hg38/bed/multiz17way/4d

    # the annotated maf is:
    ../anno/hg38.17way.maf

    # using knownGene for hg38
    hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene" hg38 > hg38.knownGene.gp

    genePredSingleCover hg38.knownGene.gp stdout | sort > hg38.knownGeneNR.gp
    wc -l *
    #  104178 hg38.knownGene.gp
    #   21887 hg38.knownGeneNR.gp

    mkdir annoSplit
    cd annoSplit
    time mafSplit -verbose=2 -outDirDepth=1 -byTarget -useFullSequenceName \
        /dev/null . ../../anno/hg38.17way.maf
    # real    21m9.120s

    find . -type f | wc -l
    #   358
    ssh ku
    mkdir /hive/data/genomes/hg38/bed/multiz17way/4d/run
    cd /hive/data/genomes/hg38/bed/multiz17way/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/multiz17way"
set c = $1:r
set infile = $r/4d/annoSplit/$2
set outDir = $r/4d/mfa/$3:h
set outfile = $r/4d/mfa/$3
/bin/mkdir -p $outDir
cd /scratch/tmp
/bin/awk -v C=$c '$2 == C {print}' $r/4d/hg38.knownGeneNR.gp | sed -e "s/\t$c\t/\thg38.$c\t/" > $c.gp
set NL=`wc -l $c.gp| gawk '{print $1}'`
echo $NL
if ("$NL" != "0") then
    $PHASTBIN/msa_view --4d --features $c.gp -i MAF $infile -o SS > $c.ss
    $PHASTBIN/msa_view -i SS --tuple-size 1 $c.ss > $outfile
else
    echo "" > $outfile
endif
/bin/rm -f $c.gp $c.ss
'_EOF_'
    # << happy emacs
    chmod +x 4d.csh

    find ../annoSplit -type f | sed -e "s#../annoSplit/##" > maf.list

    cat << '_EOF_' > template
#LOOP
4d.csh $(file1) $(path1) {check out line+ ../mfa/$(dir1)/$(root1).mfa}
#ENDLOOP
'_EOF_'
    # << happy emacs

    gensub2 maf.list single template jobList
    para create jobList
    para try ... check
    para time
# Completed: 358 of 358 jobs
# CPU time in finished jobs:       1937s      32.28m     0.54h    0.02d  0.000 y
# IO & Wait Time:                  1130s      18.84m     0.31h    0.01d  0.000 y
# Average job time:                   9s       0.14m     0.00h    0.00d
# Longest finished job:             168s       2.80m     0.05h    0.00d
# Submission to last job:           183s       3.05m     0.05h    0.00d


    # Not all results have contents, that is OK

    # combine mfa files
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz17way/4d
    # remove the broken empty files, size 0 and size 1:
    find ./mfa -type f -size 0 | xargs rm -f
    # most interesting, this did not identify files of size 1:
#    find ./mfa -type f -size 1
    find ./mfa -type f | xargs ls -og | awk '$3 == 1' | awk '{print $NF}' \
        > empty.list
    cat empty.list | xargs rm -f
    #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    0m6.633s

    # check they are all in there:
    grep "^>" 4d.all.mfa | wc -l
    # 17
    grep "^>" 4d.all.mfa | sed -e 's/^/# /;'
# >hg38
# >panTro4
# >panPan1
# >gorGor3
# >ponAbe2
# >nomLeu3
# >rheMac3
# >macFas5
# >papAnu2
# >chlSab2
# >nasLar1
# >rhiRox1
# >calJac3
# >saiBol1
# >tarSyr2
# >micMur1
# >otoGar3

    sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \
	../hg38.17way.nh | xargs echo | sed -e 's/ //g' > tree_commas.nh
    # tree_commas.nh looks like:
    #  (((((((((hg38,panTro4),panPan1),gorGor3),ponAbe2),nomLeu3),((((rheMac3,macFas5),papAn
    # 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    1m45.437s


    mv phyloFit.mod all.mod

    grep TREE all.mod
# TREE: (((((((((hg38:0.00985049,panTro4:0.00361135):0.00174038,panPan1:0.00271586):0.0052581,gorGor3:0.00892338):0.00924927,ponAbe2:0.0190369):0.00338937,nomLeu3:0.0233225):0.0115642,((((rheMac3:0.00356884,macFas5:0.00246595):0.00540557,papAnu2:0.00864345):0.00410664,chlSab2:0.0131078):0.00594457,(nasLar1:0.00691046,rhiRox1:0.00654057):0.0119771):0.0217907):0.0213423,(calJac3:0.035745,saiBol1:0.0330271):0.0381045):0.0628501,tarSyr2:0.143141):0.020665,(micMur1:0.0926521,otoGar3:0.131465):0.020665);
# TREE: (((((((((hg38:0.00986511,panTro4:0.00362765):0.0018003,panPan1:0.00273917):0.00527279,gorGor3:0.00894443):0.00928198,ponAbe2:0.0190773):0.00342227,nomLeu3:0.0233089):0.0116584,((((rheMac3:0.00357475,macFas5:0.00247387):0.00541179,papAnu2:0.00864896):0.0040728,chlSab2:0.0131272):0.006142,(nasLar1:0.00152029,rhiRox1:0.00150816):0.0180636):0.0215198):0.0213244,(calJac3:0.035743,saiBol1:0.0330514):0.0381337):0.0627813,tarSyr2:0.143207):0.0206979,(micMur1:0.0926543,otoGar3:0.131358):0.0206979);

    # compare these calculated lengths to the tree extracted from 183way:
    grep TREE all.mod | sed -e 's/TREE: //' \
       | /cluster/bin/phast/all_dists /dev/stdin | grep hg38 \
          | sed -e "s/hg38.//;"  | sort > new.dists
    /cluster/bin/phast/all_dists ../hg38.17way.nh | grep hg38 \
        | sed -e "s/hg38.//;" | sort > old.dists
    # printing out the 'new', the 'old' the 'difference' and percent difference
    join new.dists old.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 -k3n
#       panTro4 0.013462        0.013390        0.000072        0.537715
#       panPan1 0.014307        0.015610        -0.001303       -8.347213
#       gorGor3 0.025772        0.017734        0.008038        45.325364
#       ponAbe2 0.045135        0.037403        0.007732        20.672139
#       nomLeu3 0.052810        0.044204        0.008606        19.468826
#       macFas5 0.080765        0.071575        0.009190        12.839679
#       rhiRox1 0.081360        0.068974        0.012386        17.957491
#       papAnu2 0.081537        0.071626        0.009911        13.837154
#       nasLar1 0.081730        0.068974        0.012756        18.493925
#       rheMac3 0.081868        0.071575        0.010293        14.380720
#       chlSab2 0.081895        0.070974        0.010921        15.387325
#       saiBol1 0.133526        0.085804        0.047722        55.617454
#       calJac3 0.136244        0.125454        0.010790        8.600762
#       micMur1 0.259226        0.234534        0.024692        10.528111
#       tarSyr2 0.268385        0.219294        0.049091        22.385929
#       otoGar3 0.298039        0.268334        0.029705        11.070159

#########################################################################
# phastCons 17-way (DONE - 2015-02-27 - Hiram)
    # split 17way mafs into 10M chunks and generate sufficient statistics
    # files for # phastCons
    ssh ku
    mkdir -p /hive/data/genomes/hg38/bed/multiz17way/cons/SS
    cd /hive/data/genomes/hg38/bed/multiz17way/cons/SS
    mkdir result done

    cat << '_EOF_' > mkSS.csh
#!/bin/csh -ef
set d = $1
set c = $2
set doneDir = done/$d
set MAF = /hive/data/genomes/hg38/bed/multiz17way/anno/result/$d/$c.maf
set WINDOWS = /hive/data/genomes/hg38/bed/multiz17way/cons/SS/result/$d/$c
set WC = `cat $MAF | wc -l`
set NL = `grep "^#" $MAF | wc -l`
if ( -s $3 ) then
    exit 0
endif
if ( -s $3.running ) then
    exit 0
endif

/bin/mkdir -p $doneDir
/bin/date >> $3.running

/bin/rm -fr $WINDOWS
/bin/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 10000000,0 -I 1000 -B 5000
endif
popd > /dev/null
/bin/date >> $3
/bin/rm -f $3.running
'_EOF_'
    # << happy emacs
    chmod +x mkSS.csh

    cat << '_EOF_' > template
#LOOP
mkSS.csh $(dir1) $(root1) {check out line+ done/$(dir1)/$(root1)}
#ENDLOOP
'_EOF_'
    # << happy emacs

    find ../../anno/result -type f | sed -e "s#../../anno/result/##" > maf.list

    gensub2 maf.list single template jobList
    # beware overloaded the cluster with these fast running high I/O jobs
    para create jobList
    para try ... check ... etc
# Completed: 358 of 358 jobs
# CPU time in finished jobs:       3320s      55.34m     0.92h    0.04d  0.000 y
# IO & Wait Time:                  1269s      21.15m     0.35h    0.01d  0.000 y
# Average job time:                  13s       0.21m     0.00h    0.00d
# Longest finished job:             306s       5.10m     0.09h    0.00d
# Submission to last job:           506s       8.43m     0.14h    0.01d

    find ./result -type f | wc -l
    #	 645

    # 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/multiz17way/cons/run.cons
    cd /hive/data/genomes/hg38/bed/multiz17way/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 d = $2
set f = $3
set len = $4
set cov = $5
set rho = $6
set grp = $cwd:t
set cons = /hive/data/genomes/hg38/bed/multiz17way/cons
set tmp = $cons/tmp/${d}_${c}
mkdir -p $tmp
set ssSrc = $cons/SS/result
set useGrp = "$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 $ssSrc/$d/$f $tmp
else
  ln -s $ssSrc/$d/$f $tmp
  ln -s $cons/$grp/$grp.mod $tmp
endif
pushd $tmp > /dev/null
if (-s $grp.non-inf) then
  $PHASTBIN/phastCons $f $useGrp \
    --rho $rho --expected-length $len --target-coverage $cov --quiet \
    --not-informative `cat $grp.non-inf` \
    --seqname $c --idpref $c --most-conserved $c.bed --score > $c.pp
else
  $PHASTBIN/phastCons $f $useGrp \
    --rho $rho --expected-length $len --target-coverage $cov --quiet \
    --seqname $c --idpref $c --most-conserved $c.bed --score > $c.pp
endif
popd > /dev/null
mkdir -p pp/$d bed/$d
sleep 4
touch pp/$d bed/$d
rm -f pp/$d/$c.pp
rm -f bed/$d/$c.bed
mv $tmp/$c.pp pp/$d
mv $tmp/$c.bed bed/$d
rm -fr $tmp
rmdir --ignore-fail-on-non-empty $cons/tmp/$d:h
'_EOF_'
    # << happy emacs
    chmod +x doPhast.csh

    #	this template will serve for all runs
    #	root1 == chrom name, file1 == ss file name without .ss suffix
    cat << '_EOF_' > template
#LOOP
../run.cons/doPhast.csh $(root1) $(dir1) $(file1) 45 0.3 0.3 {check out line+ pp/$(dir1)/$(root1).pp}
#ENDLOOP
'_EOF_'
    # << happy emacs

    find ../SS/result -type f | sed -e "s#../SS/result/##" > ss.list
    wc -l ss.list
    #	645 ss.list

    # Create parasol batch and run it
    # run for all species
    cd /hive/data/genomes/hg38/bed/multiz17way/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 create jobList
    para try ... check ...
    para push
# Completed: 645 of 645 jobs
# CPU time in finished jobs:       8797s     146.62m     2.44h    0.10d  0.000 y
# IO & Wait Time:                  4077s      67.95m     1.13h    0.05d  0.000 y
# Average job time:                  20s       0.33m     0.01h    0.00d
# Longest finished job:              40s       0.67m     0.01h    0.00d
# Submission to last job:           188s       3.13m     0.05h    0.00d

    # create Most Conserved track
    cd /hive/data/genomes/hg38/bed/multiz17way/cons/all
    cut -f1 ../../../../chrom.sizes | while read C
do
    ls -d bed/?/${C} 2> /dev/null | while read D
    do
        echo ${D}/${C}*.bed 1>&2
        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

    /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed > mostConserved.bed
    # with the correct rhiRox1 sequence:
    # -rw-rw-r--  1 57450557 Feb 27 11:46 tmpMostConserved.bed
    # -rw-rw-r--  1 59033634 Feb 27 11:47 mostConserved.bed
    # when rhiRox1 was identical to nasLar1:
    # -rw-rw-r--  1 57441315 Dec 23 14:07 tmpMostConserved.bed
    # -rw-rw-r--  1 59023909 Dec 23 14:08 mostConserved.bed

    wc -l *.bed
    # with the correct rhiRox1 sequence:
    #   1680395 mostConserved.bed
    #   1680395 tmpMostConserved.bed
    # when rhiRox1 was identical to nasLar1:
    # 1680103 mostConserved.bed
    # 1680103 tmpMostConserved.bed

    # load into database
    ssh hgwdev
    cd /hive/data/genomes/hg38/bed/multiz17way/cons/all
    time hgLoadBed hg38 phastConsElements17way mostConserved.bed
    # with the correct rhiRox1 sequence:
    # Read 1680395 elements of size 5 from mostConserved.bed
    # real    0m15.113s
    # when rhiRox1 was identical to nasLar1:
    # Read 1680103 elements of size 5 from mostConserved.bed
    # real    0m14.377s

    # on human we often try for 5% overall cov, and 70% CDS cov
    # most bets are off here for that goal, these alignments are too few
    #	and too far between
    #	--rho 0.3 --expected-length 45 --target-coverage 0.3
    featureBits hg38 -enrichment knownGene:cds phastConsElements17way
    # with the correct rhiRox1 sequence:
    # knownGene:cds 1.266%, phastConsElements17way 6.056%, both 0.836%,
    # cover 66.02%, enrich 10.90x
    # when rhiRox1 was identical to nasLar1:
    # knownGene:cds 1.266%, phastConsElements17way 6.156%, both 0.838%,
    # cover 66.17%, enrich 10.75x

    # Create merged posterier probability file and wiggle track data files
    cd /hive/data/genomes/hg38/bed/multiz17way/cons/all
    mkdir downloads

    # the third sed fixes the chrom names, removing the partition extensions
    time (find ./pp -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 \
	| sed -e 's/\.[0-9][0-9]*-[0-9][0-9]* start/ start/' \
        | gzip -c > downloads/phastCons17way.wigFix.gz)
    #   real    35m17.514s

    # check integrity of data with wigToBigWig
    time (zcat downloads/phastCons17way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/hg38/chrom.sizes \
	    phastCons17way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=65232: VmPeak:    33796560 kB
    # real    42m14.152s

    bigWigInfo phastCons17way.bw | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 5,585,809,568
# primaryIndexSize: 93,404,096
# zoomLevels: 10
# chromCount: 357
# basesCovered: 2,948,527,266
# mean: 0.151997
# min: 0.000000
# max: 1.000000
# std: 0.253685

    #	encode those files into wiggle data
    time (zcat downloads/phastCons17way.wigFix.gz \
	| wigEncode stdin phastCons17way.wig phastCons17way.wib)
    #   Converted stdin, upper limit 1.00, lower limit 0.00
    #   real    15m11.743s

    du -hsc *.wi?
    # 2.8G    phastCons17way.wib
    # 285M    phastCons17way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phastCons17way.wib /gbdb/hg38/multiz17way/phastCons17way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz17way \
	hg38 phastCons17way phastCons17way.wig
    #   real    0m32.992s

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

    wigTableStats.sh hg38 phastCons17way
# db.table          min max mean       count sumData      stdDev  viewLimits
hg38.phastCons17way 0 1 0.151997 2948527266 4.48166e+08 0.253685 viewLimits=0:1

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram -db=hg38 \
	-hBinSize=0.001 -hBinCount=1000 -hMinVal=0.0 -verbose=2 \
	    phastCons17way > histogram.data 2>&1
    #	real    3m43.955s

    #	create plot of histogram:

    cat << '_EOF_' | gnuplot > histo.png
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 phastCons17way track"
set xlabel " phastCons17way 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
'_EOF_'
    #	<< happy emacs

    display histo.png &

#########################################################################
# phyloP for 17-way (DONE - 2015-02-27 - Hiram)
    # run phyloP with score=LRT
    ssh ku
    mkdir /cluster/data/hg38/bed/multiz17way/consPhyloP
    cd /cluster/data/hg38/bed/multiz17way/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 BACKGROUND ../../cons/all/all.mod | awk '{printf "%0.3f\n", $3 + $4}'
    #	0.567
    /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \
	../../cons/all/all.mod 0.567 > all.mod
    # verify, the BACKGROUND should now be paired up:
    grep BACK all.mod
    #   BACKGROUND: 0.216500 0.283500 0.283500 0.216500 

    cat << '_EOF_' > doPhyloP.csh
#!/bin/csh -fe
set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin
set f = $1
set d = $f:h
set file1 = $f:t
set out = $2
set cName = $f:t:r
set grp = $cwd:t
set cons = /hive/data/genomes/hg38/bed/multiz17way/consPhyloP
set tmp = $cons/tmp/$grp/$f
/bin/rm -fr $tmp
/bin/mkdir -p $tmp
set ssSrc = "/hive/data/genomes/hg38/bed/multiz17way/cons/SS/result/$f"
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 > $file1.wigFix
popd > /dev/null
/bin/mkdir -p $out:h
sleep 4
/bin/touch $out:h
/bin/mv $tmp/$file1.wigFix $out
/bin/rm -fr $tmp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp/$d
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp/$d:h
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp
/bin/rmdir --ignore-fail-on-non-empty $cons/tmp
'_EOF_'
    # << happy emacs
    chmod +x doPhyloP.csh

    # Create list of chunks
    find ../../cons/SS/result -type f | grep ".ss$" \
	| sed -e "s/.ss$//; s#^../../cons/SS/result/##" > ss.list
    # make sure the list looks good
    wc -l ss.list
    #	645 ss.list

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

    ######################   Running all species  #######################
    # setup run for all species
    mkdir /hive/data/genomes/hg38/bed/multiz17way/consPhyloP/all
    cd /hive/data/genomes/hg38/bed/multiz17way/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 create jobList
    para try ... check ... push ... etc ...
    para time > run.time
# Completed: 645 of 645 jobs
# CPU time in finished jobs:     113336s    1888.93m    31.48h    1.31d  0.004 y
# IO & Wait Time:                  4326s      72.10m     1.20h    0.05d  0.000 y
# Average job time:                 182s       3.04m     0.05h    0.00d
# Longest finished job:             749s      12.48m     0.21h    0.01d
# Submission to last job:           838s      13.97m     0.23h    0.01d

    # back on dev
    cd /hive/data/genomes/hg38/bed/multiz17way/consPhyloP/all
    mkdir downloads

    time (find ./wigFix -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/phyloP17way.wigFix.gz)
    #   real    37m24.369s

    # check integrity of data with wigToBigWig
    time (zcat downloads/phyloP17way.wigFix.gz \
	| wigToBigWig -verbose=2 stdin /hive/data/genomes/hg38/chrom.sizes \
	phyloP17way.bw) > bigWig.log 2>&1
    egrep "real|VmPeak" bigWig.log
    # pid=80999: VmPeak:    33796564 kB
    #  real    44m8.703s

    bigWigInfo phyloP17way.bw  | sed -e 's/^/# /;'
# version: 4
# isCompressed: yes
# isSwapped: 0
# primaryDataSize: 4,962,111,001
# primaryIndexSize: 93,404,096
# zoomLevels: 10
# chromCount: 357
# basesCovered: 2,948,527,266
# mean: 0.095098
# min: -14.142000
# max: 0.756000
# std: 0.622340

    #	encode those files into wiggle data
    time (zcat downloads/phyloP17way.wigFix.gz \
	| wigEncode stdin phyloP17way.wig phyloP17way.wib)
    # Converted stdin, upper limit 0.76, lower limit -14.14
    # real    16m23.549s

    du -hsc *.wi?
    # 2.8G    phyloP17way.wib
    # 291M    phyloP17way.wig

    # Load gbdb and database with wiggle.
    ln -s `pwd`/phyloP17way.wib /gbdb/hg38/multiz17way/phyloP17way.wib
    time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz17way hg38 \
	phyloP17way phyloP17way.wig
    # real    0m32.524s

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

    wigTableStats.sh hg38 phyloP17way
# db.table      min max mean count sumData
# hg38.phyloP17way -14.142 0.756 0.0950985 2948527266 2.804e+08
#       stdDev viewLimits
#      0.62234 viewLimits=-3.0166:0.756

    #	that range is: 14.142+0.756 = 14.898 for hBinSize=0.014898

    #  Create histogram to get an overview of all the data
    time hgWiggle -doHistogram \
	-hBinSize=0.014898 -hBinCount=1000 -hMinVal=-14.142 -verbose=2 \
	    -db=hg38 phyloP17way > histogram.data 2>&1
    #   real    2m43.403s

    # 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 0.000002
# Q3 0.000116
# average 0.001163
# min 0.000000
# max 0.038998
# count 860
# total 0.999988
# standard deviation 0.003859

    #	create plot of histogram:
    cat << '_EOF_' | gnuplot > histo.png
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 phyloP17way track"
set xlabel " phyloP17way score"
set ylabel " Relative Frequency"
set y2label " Cumulative Relative Frequency (CRF)"
set y2range [0:1]
set y2tics
set xrange [-4:1]
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
'_EOF_'
    #	<< happy emacs

    display histo.png &

#############################################################################
# construct download files for 17-way (DONE - 2015-02-27 - Hiram)
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz17way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons17way
    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP17way
    mkdir /hive/data/genomes/hg38/bed/multiz17way/downloads
    cd /hive/data/genomes/hg38/bed/multiz17way/downloads
    mkdir multiz17way phastCons17way phyloP17way
    cd multiz17way
    time cp -p ../../anno/hg38.17way.maf .
    #   real    1m53.295s
    # -rw-rw-r-- 1 67644767226 Feb 26 22:15 hg38.17way.maf

    time gzip *.maf
    #   real    83m39.715s

    # -rw-rw-r-- 1 8645613136 Dec 22 14:32 hg38.17way.maf.gz

    grep TREE ../../4d/all.mod | sed -e 's/TREE: //' \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > hg38.17way.nh
    ~/kent/src/hg/utils/phyloTrees/commonNames.sh hg38.17way.nh \
      | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \
         > hg38.17way.commonNames.nh
    time md5sum *.nh *.maf.gz > md5sum.txt
    #   real    1m55.317s
    ln -s `pwd`/* \
        /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz17way

    du -hsc *.maf.gz ../../anno/hg38.17way.maf
    # 8.1G    hg38.17way.maf.gz
    # 62G     ../../anno/hg38.17way.maf

    # obtain the README.txt from hg38/multiz7way and update for this
    #   situation

    #####################################################################
    cd /hive/data/genomes/hg38/bed/multiz17way/downloads/phastCons17way

    ln -s ../../cons/all/downloads/phastCons17way.wigFix.gz \
        ./hg38.phastCons17way.wigFix.gz
    ln -s ../../cons/all/phastCons17way.bw ./hg38.phastCons17way.bw
    ln -s ../../cons/all/all.mod ./hg38.phastCons17way.mod
    time md5sum *.gz *.mod *.bw > md5sum.txt
    #   real    0m37.453s

    # obtain the README.txt from hg38/phastCons7way and update for this
    #   situation
    ln -s `pwd`/*.gz `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \
      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons17way

    #####################################################################
    cd /hive/data/genomes/hg38/bed/multiz17way/downloads/phyloP17way

    ln -s ../../consPhyloP/all/downloads/phyloP17way.wigFix.gz \
        ./hg38.phyloP17way.wigFix.gz
    ln -s ../../consPhyloP/run.phyloP/all.mod hg38.phyloP17way.mod
    ln -s ../../consPhyloP/all/phyloP17way.bw hg38.phyloP17way.bw

    time md5sum *.mod *.bw *.gz > md5sum.txt
    #   real    0m34.249s

    # obtain the README.txt from hg38/phyloP7way and update for this
    #   situation
    ln -s `pwd`/* \
      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP17way

    ###########################################################################
    ## create upstream refGene maf files
    cd /hive/data/genomes/hg38/bed/multiz17way/downloads/multiz17way
    # bash script
#!/bin/sh
export geneTbl="knownGene"
for S in 1000 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/$MACHTYPE/mafFrags hg38 multiz17way \
                stdin stdout \
                -orgs=/hive/data/genomes/hg38/bed/multiz17way/species.list \
        | gzip -c > upstream${S}.${geneTbl}.maf.gz
    echo "done upstream${S}.${geneTbl}.maf.gz"
done
    #   real    71m41.626s

    md5sum upstream*.gz >> md5sum.txt

    # obtain the README.txt from hg38/multiz7way and update for this
    #   situation
    # information for table of species in the README files, need to
    # edit it in after adding it to the end of this file:

    cat ../../species.list | tr '[ ]' '[\n]' | while read D
do
 netType=`ls ../../mafLinks/${D}/hg38.${D}.*.maf.gz | sed -e "s#.*hg38.${D}.##; s#.maf.gz##;" | sed -e 's/synNet/syntenic/; s/rbest/reciprocal best/;'`
 info=`hgsql -N -e "select organism,\" - \",scientificName,description from dbDb where name=\"$D\";" hgcentraltest`
 echo "${info} ${netType}"
done | tr '[\t]' '[ ]' >> README.txt

Human - Homo sapiens              Dec. 2013 (GRCh38/hg38)            reference
Chimp - Pan troglodytes           Feb. 2011 (CSAC 2.1.4/panTro4)      syntenic
Bonobo - Pan paniscus             May. 2012 (Max-Planck/panPan1) reciprocal best
Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3)   reciprocal best
Orangutan - Pongo pygmaeus abelii   July 2007 (WUGSC 2.0.2/ponAbe2)   syntenic
Gibbon - Nomascus leucogenys      Oct. 2012 (GGSC Nleu3.0/nomLeu3)    syntenic
Rhesus - Macaca mulatta           Oct. 2010 (BGI CR_1.0/rheMac3)      syntenic
Crab-eating macaque - Macaca fascicularis 
                          Jun 2013 (Macaca_fascicularis_5.0/macFas5)  syntenic
Baboon - Papio anubis             Mar. 2012 (Baylor Panu_2.0/papAnu2) syntenic
Green monkey - Chlorocebus sabaeus
                          Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2)  syntenic
Proboscis monkey - Nasalis larvatus
                          Nov. 2014 (Charlie1.0/nasLar1)        reciprocal best
Golden snub-nosed monkey - Rhinopithecus roxellana
                          Oct. 2014 (Rrox_v1/rhiRox1)           reciprocal best
Marmoset - Callithrix jacchus       Mar. 2009 (WUGSC 3.2/calJac3)     syntenic
Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best
Tarsier - Tarsius syrichta         
                   Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best
Mouse lemur - Microcebus murinus    Jul. 2007 (Broad/micMur1) reciprocal best
Bushbaby - Otolemur garnettii       Mar. 2011 (Broad/otoGar3) reciprocal best

    # some other symlinks were already made above
    ln -s `pwd`/upstream*.gz README.txt \
        /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz17way

#############################################################################
# hgPal downloads (DONE - 2015-03-02 - Hiram)
#   FASTA from 17-way for knownGene, refGene and knownCanonical

    ssh hgwdev
    screen -S hg38HgPal
    mkdir /hive/data/genomes/hg38/bed/multiz17way/pal
    cd /hive/data/genomes/hg38/bed/multiz17way/pal
    cat ../species.list | tr '[ ]' '[\n]' > order.list

    export mz=multiz17way
    export gp=knownGene
    export db=hg38
    export I=0
    mkdir exonAA exonNuc
    for C in `sort -nk2 ../../../chrom.sizes | cut -f1`
    do
        I=`echo $I | awk '{print $1+1}'`
	echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/$C.exonNuc.fa.gz &"
	echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/$C.exonAA.fa.gz &"
        if [ $I -gt 6 ]; 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    33m25.422s

    time zcat exonAA/*.gz | gzip -c > $gp.$mz.exonAA.fa.gz
    #   real    0m40.869s
    time zcat exonNuc/*.gz | gzip -c > $gp.$mz.exonNuc.fa.gz
    #   real    2m0.836s

    export mz=multiz17way
    export gp=knownGene
    export db=hg38
    export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments
    mkdir -p $pd
    md5sum *.fa.gz > md5sum.txt
    ln -s `pwd`/$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/

    rm -rf exonAA exonNuc

    ### need other gene track alignments also
    # running up refGene
    cd /hive/data/genomes/hg38/bed/multiz17way/pal
    export mz=multiz17way
    export gp=refGene
    export db=hg38
    export I=0
    mkdir exonAA exonNuc
    for C in `sort -nk2 ../../../chrom.sizes | cut -f1`
    do
        I=`echo $I | awk '{print $1+1}'`
	echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/$C.exonNuc.fa.gz &"
	echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/$C.exonAA.fa.gz &"
        if [ $I -gt 6 ]; 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    20m17.242s

    export mz=multiz17way
    export gp=refGene
    export db=hg38
    time zcat exonAA/*.gz | gzip -c > $gp.$mz.exonAA.fa.gz
    #   real    0m33.580s
    time zcat exonNuc/*.gz | gzip -c > $gp.$mz.exonNuc.fa.gz
    #   real    1m26.819s

    du -hsc exonAA exonNuc refGene*.fa.gz
    # 126M    exonAA
    # 189M    exonNuc
    # 126M    refGene.multiz17way.exonAA.fa.gz
    # 189M    refGene.multiz17way.exonNuc.fa.gz

    rm -rf exonAA exonNuc

    # we're only distributing exons at the moment
    export mz=multiz17way
    export gp=refGene
    export db=hg38
    export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments
    mkdir -p $pd
    md5sum *.fa.gz > md5sum.txt
    ln -s `pwd`/$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/

    ### And knownCanonical
    cd /hive/data/genomes/hg38/bed/multiz17way/pal
    export mz=multiz17way
    export gp=knownCanonical
    export db=hg38
    mkdir exonAA exonNuc ppredAA ppredNuc knownCanonical

    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  $db $mz knownGene order.list stdout | \
	    gzip -c > ppredAA/$C.ppredAA.fa.gz"
	echo "mafGene -geneBeds=knownCanonical/$C.known.bed -noTrans $db $mz knownGene order.list stdout | \
	    gzip -c > ppredNuc/$C.ppredNuc.fa.gz"
	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
    # real    92m43.125s


    rm *.known.bed
    export mz=multiz17way
    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 &
    zcat ppredAA/c*.gz | gzip -c > $gp.$mz.ppredAA.fa.gz &
    zcat ppredNuc/c*.gz | gzip -c > $gp.$mz.ppredNuc.fa.gz

    rm -rf exonAA exonNuc ppredAA ppredNuc

    export mz=multiz17way
    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
    cd  $pd
    md5sum *.exon*.fa.gz > md5sum.txt

#############################################################################
# wiki page for 17-way (DONE - 2014-06-04 - Hiram)
    mkdir /hive/users/hiram/bigWays/hg38.17way
    cd /hive/users/hiram/bigWays
    echo "hg38" > hg38.17way/ordered.list
    awk '{print $1}' /hive/data/genomes/hg38/bed/multiz17way/17way.distances.txt \
       >> hg38.17way/ordered.list

    # sizeStats.sh catches up the cached measurements required for data
    # in the tables.  They may already be done.
    ./sizeStats.sh hg38.17way/ordered.list
    # dbDb.sh constructs hg38.17way/Hg38_17-way_conservation_alignment.html
    ./dbDb.sh hg38 17way
    # sizeStats.pl constructs hg38.17way/Hg38_17-way_Genome_size_statistics.html
    ./sizeStats.pl hg38 17way

    # defCheck.pl constructs Hg38_17-way_conservation_lastz_parameters.html
    ./defCheck.pl hg38 17way

    # this constructs the html pages in hg38.17way/:
# -rw-rw-r-- 1 4153 Jun  5 11:03 Hg38_17-way_conservation_alignment.html
# -rw-rw-r-- 1 5833 Jun  5 11:04 Hg38_17-way_Genome_size_statistics.html
# -rw-rw-r-- 1 3854 Jun  5 11:04 Hg38_17-way_conservation_lastz_parameters.html

    # add those pages to the genomewiki.  Their page names are the
    # names of the .html files without the .html:
#  Hg38_17-way_conservation_alignment
#  Hg38_17-way_Genome_size_statistics
#  Hg38_17-way_conservation_lastz_parameters

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

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