c856e12e25aa93d1ec5095fbb720b6b564f4a550
hiram
  Wed Jul 3 11:35:38 2019 -0700
ready to start genbank run refs #23771

diff --git src/hg/makeDb/doc/rheMac10/initialBuild.txt src/hg/makeDb/doc/rheMac10/initialBuild.txt
new file mode 100644
index 0000000..9e6c0d4
--- /dev/null
+++ src/hg/makeDb/doc/rheMac10/initialBuild.txt
@@ -0,0 +1,1002 @@
+# for emacs: -*- mode: sh; -*-
+
+# This file describes browser build for the rheMac10
+
+#  Can use existing photograph (otherwise find one before starting here)
+
+#########################################################################
+#  Initial steps, reuse existing photograph (DONE - 2019-07-01 - Hiram)
+
+# To start this initialBuild.txt document, from a previous assembly document:
+
+mkdir ~/kent/src/hg/makeDb/doc/rheMac10
+cd ~/kent/src/hg/makeDb/doc/rheMac10
+
+sed -e 's/galGal6/rheMac10/g; s/GalGal6/RheMac10/g; s/DONE/TBD/g;' \
+  ../galGal6/initialBuild.txt > initialBuild.txt
+
+mkdir -p /hive/data/genomes/rheMac10/refseq
+cd /hive/data/genomes/rheMac10
+
+#  Can use existing photograph
+cp -p ../rn6/photoReference.txt ./
+cat photoReference.txt
+photoCreditURL  http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Rat%20(brown%20norway)&id=79111
+photoCreditName NHGRI press photos
+
+## download from NCBI
+cd /hive/data/genomes/rheMac10/refseq
+
+time rsync -L -a -P --stats \
+rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_mulatta/all_assembly_versions/GCF_003339765.1_Mmul_10/ ./
+
+# sent 3,937 bytes  received 6,369,691,679 bytes  56,619,516.59 bytes/sec
+# total size is 6,368,121,788  speedup is 1.00
+
+# real    1m51.641s
+
+# this information is from the top of 
+#    rheMac10/refseq/*_assembly_report.txt
+#    (aka: rheMac10/refseq/GCF_003339765.1_Mmul_10_assembly_report.txt
+
+# Assembly name:  Mmul_10
+# Organism name:  Macaca mulatta (Rhesus monkey)
+# Taxid:          9544
+# BioSample:      SAMN09435472
+# BioProject:     PRJNA476474
+# Submitter:      The Genome Institute at Washington University School of Medicine
+# Date:           2019-02-13
+# Assembly type:  haploid
+# Release type:   major
+# Assembly level: Chromosome
+# Genome representation: full
+# WGS project:    QNVO02
+# GenBank assembly accession: GCA_003339765.3
+# RefSeq assembly accession: GCF_003339765.1
+# RefSeq assembly and GenBank assemblies identical: no
+#
+## Assembly-Units:
+## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
+## GCA_003339795.3      GCF_003339795.1 Primary Assembly
+##      GCF_000005875.1 non-nuclear
+#
+
+# check assembly size for later reference:
+
+faSize G*10_genomic.fna.gz
+# 2971331530 bases (34438805 N's 2936892725 real 1810047126 upper
+#	1126845599 lower) in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (NW_021162293.1)
+#	max 223616942 (NC_041754.1) median 26547
+# %37.92 masked total, %38.37 masked real
+
+#############################################################################
+# establish config.ra file (DONE - Hiram - 2019-07-01)
+    cd /hive/data/genomes/rheMac10
+    ~/kent/src/hg/utils/automation/prepConfig.pl rheMac10 primate rhesus \
+       refseq/*_assembly_report.txt > rheMac10.config.ra
+
+    # compare with previous version to see if it is sane:
+    diff rheMac10.config.ra ../rheMac8/rheMac8.config.ra
+
+    # verify it really does look sane
+    cat rheMac10.config.ra
+# config parameters for makeGenomeDb.pl:
+db rheMac10
+clade primate
+genomeCladePriority 35
+scientificName Macaca mulatta
+commonName rhesus
+assemblyDate Feb. 2019
+assemblyLabel The Genome Institute at Washington University School of Medicine
+assemblyShortLabel Mmul_10
+orderKey 18417
+# mitochondrial sequence included in refseq release
+# mitoAcc NC_005943.1
+mitoAcc none
+fastaFiles /hive/data/genomes/rheMac10/ucsc/*.fa.gz
+agpFiles /hive/data/genomes/rheMac10/ucsc/*.agp
+# qualFiles none
+dbDbSpeciesDir rhesus
+photoCreditURL  http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Rat%20(brown%20norway)&id=79111
+photoCreditName NHGRI press photos
+ncbiGenomeId 215
+ncbiAssemblyId 2345051
+ncbiAssemblyName Mmul_10
+ncbiBioProject 476474
+ncbiBioSample SAMN09435472
+genBankAccessionID GCF_003339765.1
+taxId 9544
+
+#############################################################################
+# setup UCSC named files (DONE - 2019-07-01 - Hiram)
+
+    mkdir /hive/data/genomes/rheMac10/ucsc
+    cd /hive/data/genomes/rheMac10/ucsc
+
+    # check for duplicate sequences:
+    time faToTwoBit -noMask ../refseq/G*10_genomic.fna.gz refseq.2bit
+    #  real    0m38.595s
+
+    twoBitDup refseq.2bit
+    # no output is a good result, otherwise, would have to eliminate duplicates
+    # the scripts creating the fasta here will be using this refseq.2bit file
+    # remove it later
+
+    # new option required to ucscCompositeAgp.pl 2016-04-13
+    time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \
+      ../refseq/G*10_genomic.fna.gz \
+	../refseq/*_assembly_structure/Primary_Assembly
+# constructing refseq.2bit from ../refseq/GCF_000002315.4_Gallus_gallus-5.0_genomic.fna.gz
+NC_027914.1 chrY
+NC_041754.1 chr1
+NC_041755.1 chr2
+NC_041756.1 chr3
+NC_041757.1 chr4
+NC_041758.1 chr5
+NC_041759.1 chr6
+NC_041760.1 chr7
+NC_041761.1 chr8
+NC_041762.1 chr9
+NC_041763.1 chr10
+NC_041764.1 chr11
+NC_041765.1 chr12
+NC_041766.1 chr13
+NC_041767.1 chr14
+NC_041768.1 chr15
+NC_041769.1 chr16
+NC_041770.1 chr17
+NC_041771.1 chr18
+NC_041772.1 chr19
+NC_041773.1 chr20
+NC_041774.1 chrX
+
+real    10m33.076s
+
+    time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \
+       ../refseq/*_assembly_structure/Primary_Assembly
+    # processed 340 sequences into chrUn.fa.gz
+    # real    0m30.432s
+
+    time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \
+       ../refseq/*_assembly_structure/Primary_Assembly
+# 11
+# 7
+# 17
+# 2
+# 1
+# 18
+# 16
+# 13
+# 6
+# X
+# 3
+# 9
+# 12
+# 20
+# 14
+# 15
+# 8
+# 4
+# 19
+# 10
+# 5
+# processed 291 sequences into chr*_random.gz 21 files
+
+real    0m7.023s
+
+    # bash syntax here
+    mitoAcc=`grep "^# mitoAcc" ../rheMac10.config.ra | awk '{print $NF}'`
+    printf "# mitoAcc %s\n" "$mitoAcc"
+# mitoAcc NC_005943.1
+
+    zcat \
+  ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \
+     | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp
+
+    cat chrM.agp
+# chrM    1       16564   1       O       NC_005943.1     1       16564   +
+
+    printf ">chrM\n" > chrM.fa
+    twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa
+    gzip chrM.fa
+
+    faSize chrM.fa.gz
+# 16564 bases (0 N's 16564 real 16564 upper 0 lower) in 1 sequences in 1 files
+
+    # verify fasta and AGPs agree
+    time faToTwoBit *.fa.gz test.2bit
+    # real    0m56.726s
+
+    cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4
+    # All AGP and FASTA entries agree - both files are valid
+
+    # and no sequence lost from orginal:
+    twoBitToFa test.2bit stdout | faSize stdin
+# 2971331530 bases (34438805 N's 2936892725 real 2936892725 upper 0 lower)
+#	in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1)
+#	max 223616942 (chr1) median 26547
+
+    # same numbers as above (except for upper/lower masking)
+# 2971331530 bases (34438805 N's 2936892725 real 1810047126 upper
+#	1126845599 lower) in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (NW_021162293.1)
+#	max 223616942 (NC_041754.1) median 26547
+
+    # no longer need these temporary 2bit files
+    rm test.2bit refseq.2bit
+
+#############################################################################
+#  Initial database build (DONE - 2019-07-01 - Hiram)
+
+    # verify sequence and AGP are OK:
+    cd /hive/data/genomes/rheMac10
+    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
+         -stop=agp rheMac10.config.ra) > agp.log 2>&1
+    # real    2m22.570s
+
+    # then finish it off:
+    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
+       -fileServer=hgwdev -continue=db rheMac10.config.ra) > db.log 2>&1
+    # real    15m24.340s
+
+    # check in the trackDb files created in TemporaryTrackDbCheckout/
+    #    and add rheMac10 to trackDb/makefile
+
+    # temporary symlink until masked sequence is available
+    cd /hive/data/genomes/rheMac10
+    ln -s `pwd`/rheMac10.unmasked.2bit /gbdb/rheMac10/rheMac10.2bit
+
+##############################################################################
+# cpgIslands on UNMASKED sequence (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/cpgIslandsUnmasked
+    cd /hive/data/genomes/rheMac10/bed/cpgIslandsUnmasked
+
+    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
+       -tableName=cpgIslandExtUnmasked \
+          -maskedSeq=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit \
+             -workhorse=hgwdev -smallClusterHub=ku rheMac10) > do.log 2>&1
+    # real    3m25.609s
+
+    cat fb.rheMac10.cpgIslandExtUnmasked.txt
+    # 38819797 bases of 2936892733 (1.322%) in intersection
+
+#############################################################################
+# cytoBandIdeo - (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/cytoBand
+    cd /hive/data/genomes/rheMac10/bed/cytoBand
+    makeCytoBandIdeo.csh rheMac10
+
+#############################################################################
+# run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/idKeys
+    cd /hive/data/genomes/rheMac10/bed/idKeys
+
+    time (doIdKeys.pl \
+        -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit \
+        -buildDir=`pwd` rheMac10) > do.log 2>&1 &
+    # real    4m9.394s
+
+    cat rheMac10.keySignature.txt
+    #  69c74f5fa18fe2421cabbcd0e80657e9
+
+#############################################################################
+# gapOverlap (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/gapOverlap
+    cd /hive/data/genomes/rheMac10/bed/gapOverlap
+    time (doGapOverlap.pl \
+        -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit rheMac10 ) \
+        > do.log 2>&1 &
+    # real    1m3.768s
+
+    # there is only one:
+    wc -l bed.tab
+    # 1 bed.tab
+    cut -f2- bed.tab
+chr4    51027118        51073686        chr4:51027119-51073686  1000    +      51027118 51073686        0       2       1000,1000       0,45568
+
+    cat fb.rheMac10.gapOverlap.txt
+    # 2000 bases of 2971331530 (0.000%) in intersection
+
+#############################################################################
+# tandemDups (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/tandemDups
+    cd /hive/data/genomes/rheMac10/bed/tandemDups
+    time (~/kent/src/hg/utils/automation/doTandemDup.pl \
+  -twoBit=/hive/data/genomes/rheMac10/rheMac10.unmasked.2bit rheMac10) \
+        > do.log 2>&1 &
+    # real    225m10.394s
+
+    cat fb.rheMac10.tandemDups.txt
+    # 81485851 bases of 2971331530 (2.742%) in intersection
+
+    bigBedInfo rheMac10.tandemDups.bb | sed -e 's/^/#  /;'
+#  version: 4
+#  fieldCount: 13
+#  hasHeaderExtension: yes
+#  isCompressed: yes
+#  isSwapped: 0
+#  extraIndexCount: 0
+#  itemCount: 1,431,488
+#  primaryDataSize: 37,737,612
+#  primaryIndexSize: 176,456
+#  zoomLevels: 9
+#  chromCount: 2756
+#  basesCovered: 1,568,894,232
+#  meanDepth (of bases covered): 8.122557
+#  minDepth: 1.000000
+#  maxDepth: 314.000000
+#  std of depth: 13.438018
+
+#########################################################################
+# ucscToINSDC and ucscToRefSeq table/track (DONE - 2019-07-01 - Hiram)
+    # construct idKeys for the refseq sequence
+    mkdir /hive/data/genomes/rheMac10/refseq/idKeys
+    cd /hive/data/genomes/rheMac10/refseq/idKeys
+    faToTwoBit ../GCF_003339765.1_Mmul_10_genomic.fna.gz rheMac10.refSeq.2bit
+
+    time (doIdKeys.pl -buildDir=`pwd` \
+        -twoBit=`pwd`/rheMac10.refSeq.2bit refseqRheMac10)  > do.log 2>&1 &
+    # real    4m8.863s
+
+    cat refseqRheMac10.keySignature.txt
+    #  69c74f5fa18fe2421cabbcd0e80657e9
+
+    # and the genbank sequence needs keys too:
+    mkdir /hive/data/genomes/rheMac10/refseq/idKeysGenbank
+    cd /hive/data/genomes/rheMac10/refseq/idKeysGenbank
+    faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Macaca_mulatta/all_assembly_versions/GCA_003339765.3_Mmul_10/GCA_003339765.3_Mmul_10_genomic.fna.gz rheMac10.genbank.2bit
+
+    time (doIdKeys.pl -buildDir=`pwd` \
+        -twoBit=`pwd`/rheMac10.genbank.2bit genbankRheMac10)  > do.log 2>&1 &
+    # real    4m6.755s
+
+
+    cat genbankRheMac10.keySignature.txt
+    #  1eb34462822483c9262e98186f71a286
+
+    mkdir /hive/data/genomes/rheMac10/bed/chromAlias
+    cd /hive/data/genomes/rheMac10/bed/chromAlias
+
+    join -t$'\t' ../idKeys/rheMac10.idKeys.txt \
+        ../../refseq/idKeysGenbank/genbankRheMac10.idKeys.txt | cut -f2- \
+          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
+            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
+               | sort -k1,1 -k2,2n > ucscToINSDC.bed
+
+    join -t$'\t' ../idKeys/rheMac10.idKeys.txt \
+        ../../refseq/idKeys/refseqRheMac10.idKeys.txt | cut -f2- \
+          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
+            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
+               | sort -k1,1 -k2,2n > ucscToRefSeq.bed
+
+    # should be same line counts throughout:
+    wc -l * ../../chrom.sizes
+    # 2938 ucscToINSDC.bed
+    # 2939 ucscToRefSeq.bed
+    # 2939 ../../chrom.sizes
+
+    # need to find the accession for the INSDC equivalent to chrM:
+    egrep chrM *
+# ucscToRefSeq.bed:chrM   0       16564   NC_005943.1
+
+    # lookup that accession at NCBI Entrez: AY612638.1
+    # and add to ucscToINSDC.bed:
+    printf "chrM\t0\t16564\tAY612638.1\n" >> ucscToINSDC.bed
+    # verify:
+    grep chrM *
+ucscToINSDC.bed:chrM    0       16564   AY612638.1
+ucscToRefSeq.bed:chrM   0       16564   NC_005943.1
+
+    export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1`
+    echo $chrSize
+    # 27
+    # use the $chrSize in this sed
+    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
+         | hgLoadSqlTab rheMac10 ucscToINSDC stdin ucscToINSDC.bed
+     # should be the same for ucscToRefSeq:
+    export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1`
+    echo $chrSize
+    # 27
+    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
+       | sed -e 's/INSDC/RefSeq/g;' \
+         | hgLoadSqlTab rheMac10 ucscToRefSeq stdin ucscToRefSeq.bed
+
+    # should be quiet for all OK
+    checkTableCoords rheMac10
+
+    # should cover %100 entirely:
+    featureBits -countGaps rheMac10 ucscToINSDC
+    # 2971331530 bases of 2971331530 (100.000%) in intersection
+    featureBits -countGaps rheMac10 ucscToRefSeq
+    # 2971331530 bases of 2971331530 (100.000%) in intersection
+
+#########################################################################
+# add chromAlias table (DONE - 2019-07-01 - Hiram)
+
+    mkdir /hive/data/genomes/rheMac10/bed/chromAlias
+    cd /hive/data/genomes/rheMac10/bed/chromAlias
+
+    hgsql -N -e 'select chrom,name from ucscToRefSeq;' rheMac10 \
+        | sort -k1,1 > ucsc.refseq.tab
+    hgsql -N -e 'select chrom,name from ucscToINSDC;' rheMac10 \
+        | sort -k1,1 > ucsc.genbank.tab
+
+    ### Adding Ensembl alias with v95 release, after idKeys made: 2019-01-16
+    join -t$'\t' ../idKeys/rheMac10.idKeys.txt \
+        ../../ens95/ensRheMac10.idKeys.txt | cut -f2- \
+          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
+            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
+               | sort -k1,1 -k2,2n > ucscToEns.bed
+    cut -f1,4 ucscToEns.bed | sort > ucsc.ensembl.tab
+    wc -l *.bed
+#   2210 ucscToEns.bed
+#   2211 ucscToINSDC.bed
+#   2211 ucscToRefSeq.bed
+
+    ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
+        > rheMac10.chromAlias.tab
+
+for t in refseq genbank
+do
+  c0=`cat ucsc.$t.tab | wc -l`
+  c1=`grep $t rheMac10.chromAlias.tab | wc -l`
+  ok="OK"
+  if [ "$c0" -ne "$c1" ]; then
+     ok="ERROR"
+  fi
+  printf "# checking $t: $c0 =? $c1 $ok\n"
+done
+# checking refseq: 2939 =? 2939 OK
+# checking genbank: 2939 =? 2939 OK
+
+    # verify chrM is here properly:
+    grep chrM rheMac10.chromAlias.tab 
+# AY612638.1      chrM    genbank
+# NC_005943.1     chrM    refseq
+
+    hgLoadSqlTab rheMac10 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
+        rheMac10.chromAlias.tab
+
+#########################################################################
+# fixup search rule for assembly track/gold table (TBD - 2019-07-01 - Hiram)
+    cd ~/kent/src/hg/makeDb/trackDb/rhesus/rheMac10
+    # preview prefixes and suffixes:
+    hgsql -N -e "select frag from gold;" rheMac10 \
+      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 
+      2 AC.10
+      2 AC.11
+      1 AC.13
+      1 AC.17
+      4 AC.2
+     36 AC.3
+     22 AC.4
+      8 AC.5
+      2 AC.6
+      5 AC.7
+      4 AC.8
+      2 AC.9
+      1 NC_.1
+   3178 QNVO.1
+
+    # implies a rule: '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?'
+
+    # verify this rule will find them all and eliminate them all:
+    hgsql -N -e "select frag from gold;" rheMac10 | wc -l
+    # 3268
+
+    hgsql -N -e "select frag from gold;" rheMac10 \
+       | egrep -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l
+    # 3268
+
+    hgsql -N -e "select frag from gold;" rheMac10 \
+       | egrep -v -e '[ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?' | wc -l
+    # 0
+
+    # hence, add to trackDb/rhesus/rheMac10/trackDb.ra
+searchTable gold
+shortCircuit 1
+termRegex [ANQ][CN][V0-9_][O0-9][0-9]+(\.[0-9]+)?
+query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
+searchPriority 8
+
+XXX - TBD
+
+    # verify searches work in the position box
+
+##########################################################################
+# running repeat masker (DONE - 2019-07-01 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/repeatMasker
+    cd /hive/data/genomes/rheMac10/bed/repeatMasker
+    time  (doRepeatMasker.pl -buildDir=`pwd` \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -smallClusterHub=ku rheMac10) > do.log 2>&1
+    # real    500m43.380s
+
+    cat faSize.rmsk.txt
+# 2971331530 bases (34438805 N's 2936892725 real 1399379596 upper
+#	1537513129 lower) in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1)
+#	max 223616942 (chr1) median 26547
+# %51.74 masked total, %52.35 masked real
+
+    egrep -i "versi|relea" do.log
+# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
+#    February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker
+# CC    Dfam_Consensus RELEASE 20181026;                            *
+# CC    RepBase RELEASE 20181026;         
+
+    time featureBits -countGaps rheMac10 rmsk
+    # 1537510421 bases of 2971331530 (51.745%) in intersection
+    # real    0m40.763s
+
+    # why is it different than the faSize above ?
+    # because rmsk masks out some N's as well as bases, the faSize count above
+    #   separates out the N's from the bases, it doesn't show lower case N's
+
+    # faster way to get the same result on high contig count assemblies:
+    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' rheMac10 \
+        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
+    # total 1537510421.000000
+    # real    0m24.256s
+
+##########################################################################
+# running simple repeat (DONE - 2019-07-01 - Hiram)
+
+    # The '-trf409 5' is a bit smaller than human which is 6
+
+    mkdir /hive/data/genomes/rheMac10/bed/simpleRepeat
+    cd /hive/data/genomes/rheMac10/bed/simpleRepeat
+    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
+        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
+        -trf409=5 rheMac10) > do.log 2>&1
+    # real    933m29.936s
+
+    cat fb.simpleRepeat
+    # 158143361 bases of 2936892733 (5.385%) in intersection
+
+    cd /hive/data/genomes/rheMac10
+    # using the Window Masker result:
+    cd /hive/data/genomes/rheMac10
+#    twoBitMask bed/windowMasker/rheMac10.cleanWMSdust.2bit \
+#       -add bed/simpleRepeat/trfMask.bed  rheMac10.2bit
+    #   you can safely ignore the warning about fields >= 13
+
+    # add to rmsk after it is done:
+    twoBitMask rheMac10.rmsk.2bit \
+        -add bed/simpleRepeat/trfMask.bed rheMac10.2bit
+    #   you can safely ignore the warning about fields >= 13
+    twoBitToFa rheMac10.2bit stdout | faSize stdin > faSize.rheMac10.2bit.txt
+    cat faSize.rheMac10.2bit.txt
+# 2971331530 bases (34438805 N's 2936892725 real 1397548789 upper
+#	1539343936 lower) in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1)
+#	max 223616942 (chr1) median 26547
+# %51.81 masked total, %52.41 masked real
+
+    rm /gbdb/rheMac10/rheMac10.2bit
+    ln -s `pwd`/rheMac10.2bit /gbdb/rheMac10/rheMac10.2bit
+
+#########################################################################
+# CREATE MICROSAT TRACK (DONE - 2019-07-02 - Hiram)
+    ssh hgwdev
+    mkdir /cluster/data/rheMac10/bed/microsat
+    cd /cluster/data/rheMac10/bed/microsat
+
+    awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \
+       ../simpleRepeat/simpleRepeat.bed > microsat.bed
+
+    hgLoadBed rheMac10 microsat microsat.bed
+    # Read 32040 elements of size 4 from microsat.bed
+
+##########################################################################
+## WINDOWMASKER (DONE - 2019-07-01 - Hiram)
+
+    mkdir /hive/data/genomes/rheMac10/bed/windowMasker
+    cd /hive/data/genomes/rheMac10/bed/windowMasker
+    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
+        -dbHost=hgwdev rheMac10) > do.log 2>&1
+    # real    111m14.660s
+
+    # Masking statistics
+    cat faSize.rheMac10.cleanWMSdust.txt
+# 2971331530 bases (34438805 N's 2936892725 real 1792976685 upper
+#	1143916040 lower) in 2939 sequences in 1 files
+# Total size: mean 1011000.9 sd 12006707.4 min 217 (chrUn_NW_021162293v1)
+#	max 223616942 (chr1) median 26547
+# %38.50 masked total, %38.95 masked real
+
+    cat fb.rheMac10.rmsk.windowmaskerSdust.txt
+    # 909614480 bases of 2971331530 (30.613%) in intersection
+
+##########################################################################
+# cpgIslands - (DONE - 2019-07-02 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/cpgIslands
+    cd /hive/data/genomes/rheMac10/bed/cpgIslands
+    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
+      -workhorse=hgwdev -smallClusterHub=ku rheMac10) > do.log 2>&1
+XXX - running - Tue Jul  2 07:51:16 PDT 2019
+    # real    2m5.105s
+
+    cat fb.rheMac10.cpgIslandExt.txt
+    # 16395346 bases of 1055588482 (1.553%) in intersection
+
+##############################################################################
+# genscan - (DONE - 2019-07-02 - Hiram)
+    mkdir /hive/data/genomes/rheMac10/bed/genscan
+    cd /hive/data/genomes/rheMac10/bed/genscan
+    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
+      -bigClusterHub=ku rheMac10) > do.log 2>&1
+XXX - running - Tue Jul  2 07:51:42 PDT 2019
+    # real    88m34.900s
+
+    cat fb.rheMac10.genscan.txt
+    # 23911678 bases of 1055588482 (2.265%) in intersection
+
+    cat fb.rheMac10.genscanSubopt.txt
+    # 24521608 bases of 1055588482 (2.323%) in intersection
+
+#########################################################################
+# Create kluster run files (DONE - 2019-07-01 - Hiram)
+
+    # numerator is rheMac10 gapless bases "real" as reported by:
+    featureBits -noRandom -noHap rheMac10 gap
+    # 32449617 bases of 2821543288 (1.150%) in intersection
+    #                      ^^^
+
+    # denominator is hg19 gapless bases as reported by:
+    #   featureBits -noRandom -noHap hg19 gap
+    #     234344806 bases of 2861349177 (8.190%) in intersection
+    # 1024 is threshold used for human -repMatch:
+    calc \( 2821543288 / 2861349177 \) \* 1024
+    #  ( 2821543288 / 2861349177 ) * 1024 = 1009.754542
+
+    # ==> use -repMatch=350 according to size scaled down from 1024 for human.
+    #   and rounded down to nearest 50
+    cd /hive/data/genomes/rheMac10
+    blat rheMac10.2bit \
+         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/rheMac10.11.ooc \
+        -repMatch=1000
+    #   Wrote 31768 overused 11-mers to jkStuff/rheMac10.11.ooc
+    # rheMac8 at repMatch=900:
+    #   Wrote 43065 overused 11-mers to jkStuff/rheMac8.11.ooc
+
+    #   check non-bridged gaps to see what the typical size is:
+    hgsql -N \
+        -e 'select * from gap where bridge="no" order by size;' rheMac10 \
+        | sort -k7,7nr | ave -col=7 stdin
+    # min 100.000000
+    # max 1000000.000000
+
+    # minimum gap size is 100 and produces a reasonable number of lifts
+    gapToLift -verbose=2 -minGap=100 rheMac10 jkStuff/rheMac10.nonBridged.lft \
+        -bedFile=jkStuff/rheMac10.nonBridged.bed
+    wc -l jkStuff/rheMac10.nonBri*
+    # 2979 jkStuff/rheMac10.nonBridged.bed
+    # 2979 jkStuff/rheMac10.nonBridged.lft
+
+########################################################################
+# lastz/chain/net swap human/hg38 (TBD - 2018-10-12 - Hiram)
+    # original alignment
+    cd /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12
+
+    cat fb.hg38.chainRheMac10Link.txt
+    # 154079940 bases of 3095998939 (4.977%) in intersection
+    cat fb.hg38.chainSynRheMac10Link.txt
+    # 95877644 bases of 3095998939 (3.097%) in intersection
+    cat fb.hg38.chainRBest.RheMac10.txt
+    # 106665747 bases of 3095998939 (3.445%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/rheMac10/bed/blastz.hg38.swap
+    cd /hive/data/genomes/rheMac10/bed/blastz.hg38.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg38/bed/lastzRheMac10.2018-10-12/DEF \
+        -swap -chainMinScore=5000 -chainLinearGap=loose \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    9m45.514s
+
+    cat fb.rheMac10.chainHg38Link.txt
+    # 120955955 bases of 1055588482 (11.459%) in intersection
+
+    cat fb.rheMac10.chainSynHg38Link.txt
+    # 92597630 bases of 1055588482 (8.772%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1 &
+    # real    139m24.408s
+
+    cat fb.rheMac10.chainRBest.Hg38.txt
+    # 106294585 bases of 1055588482 (10.070%) in intersection
+
+#########################################################################
+# lastz/chain/net swap mouse/mm10 (TBD - 2018-10-12 - Hiram)
+
+    # original alignment
+    cd /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12
+    cat fb.mm10.chainRheMac10Link.txt
+    # 101151132 bases of 2652783500 (3.813%) in intersection
+    cat fb.mm10.chainSynRheMac10Link.txt
+    # 70707720 bases of 2652783500 (2.665%) in intersection
+    cat fb.mm10.chainRBest.RheMac10.txt 
+    # 79649474 bases of 2652783500 (3.002%) in intersection
+
+    # and for the swap:
+    mkdir /hive/data/genomes/rheMac10/bed/blastz.mm10.swap
+    cd /hive/data/genomes/rheMac10/bed/blastz.mm10.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/mm10/bed/lastzRheMac10.2018-10-12/DEF \
+        -swap -chainMinScore=5000 -chainLinearGap=loose \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > swap.log 2>&1
+    #  real    6m41.043s
+
+    cat fb.rheMac10.chainMm10Link.txt
+    # 88539346 bases of 1055588482 (8.388%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 &
+    # real    94m11.007s
+
+    cat fb.rheMac10.chainRBest.Mm10.txt
+    # 79474812 bases of 1055588482 (7.529%) in intersection
+
+#########################################################################
+# GENBANK AUTO UPDATE (DONE - 2019-07-03 - Hiram)
+    ssh hgwdev
+    cd $HOME/kent/src/hg/makeDb/genbank
+    git pull
+    # /cluster/data/genbank/data/organism.lst shows:
+    # #organism       mrnaCnt estCnt  refSeqCnt
+    # Macaca mulatta  381495  60276   5820
+
+    # edit etc/genbank.conf to add rheMac10 just before galGal5
+
+# rheMac10 Macaca mulatta (rhesus) (refseq assembly GCF_003339765.1)
+rheMac10.serverGenome = /hive/data/genomes/rheMac10/rheMac10.2bit
+rheMac10.ooc = /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc
+rheMac10.lift = /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft
+rheMac10.perChromTables = no
+rheMac10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
+rheMac10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
+rheMac10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
+rheMac10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
+rheMac10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
+rheMac10.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
+rheMac10.downloadDir = rheMac10
+# DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus)
+rheMac10.refseq.mrna.native.load  = yes
+rheMac10.refseq.mrna.xeno.load  = yes
+rheMac10.upstreamGeneTbl = refGene
+
+    # verify the files specified exist before checking in the file:
+  grep ^rheMac10 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og
+# -rw-rw-r-- 1    127080 Jul  1 11:03 /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc
+# -rw-rw-r-- 1    177516 Jul  1 13:16 /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft
+# -rw-rw-r-- 1 775334369 Jul  2 07:48 /hive/data/genomes/rheMac10/rheMac10.2bit
+
+    git commit -m "Added rheMac10 rhesus/Macaca mulatta; refs #23771" etc/genbank.conf
+    git push
+    # update /cluster/data/genbank/:
+    make etc-update
+
+    # enable daily alignment and update of hgwdev
+    cd ~/kent/src/hg/makeDb/genbank
+    git pull
+    # add rheMac10 to:
+    #   etc/hgwdev.dbs
+    git add etc/align.dbs etc/hgwdev.dbs
+    git commit -m "Added rheMac10 - rhesus/Macaca mulatta refs #23771" etc/hgwdev.dbs
+    git push
+    make etc-update
+
+    # wait a few days for genbank magic to take place, the tracks will
+    # appear
+
+#############################################################################
+# augustus gene track (DONE - 2019-07-02 - Hiram)
+
+    mkdir /hive/data/genomes/rheMac10/bed/augustus
+    cd /hive/data/genomes/rheMac10/bed/augustus
+    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
+        -species=human -dbHost=hgwdev \
+           -workhorse=hgwdev rheMac10) > do.log 2>&1
+XXX - running - Tue Jul  2 07:53:20 PDT 2019
+    # real    48m48.597s
+
+    cat fb.rheMac10.augustusGene.txt
+    # 25827925 bases of 1055588482 (2.447%) in intersection
+
+#########################################################################
+# ncbiRefSeq (DONE - 2019-07-02 - Hiram)
+
+    mkdir /hive/data/genomes/rheMac10/bed/ncbiRefSeq
+    cd /hive/data/genomes/rheMac10/bed/ncbiRefSeq
+    # running step wise just to be careful
+    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -bigClusterHub=ku -dbHost=hgwdev \
+      -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
+      refseq vertebrate_mammalian Macaca_mulatta \
+      GCF_003339765.1_Mmul_10 rheMac10) > download.log 2>&1
+    # real    2m3.842s
+
+    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -continue=process -bigClusterHub=ku -dbHost=hgwdev \
+      -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
+      refseq vertebrate_mammalian Macaca_mulatta \
+      GCF_003339765.1_Mmul_10 rheMac10) > process.log 2>&1
+    # real    2m6.030s
+
+    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -continue=load -bigClusterHub=ku -dbHost=hgwdev \
+      -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
+      refseq vertebrate_mammalian Macaca_mulatta \
+      GCF_003339765.1_Mmul_10 rheMac10) > load.log 2>&1
+    # real    0m27.175s
+
+    cat fb.ncbiRefSeq.rheMac10.txt
+    #  92462016 bases of 2936892733 (3.148%) in intersection
+
+XXX TBD
+    # need to add: include ../../refSeqComposite.ra alpha
+    # to the rhesus/rheMac10/trackDb.ra to turn on the track in the browser
+
+    # there was one gene that claimed to have a protein, but the
+    # protein sequence was not included in the protein.faa file
+    # discovered from joinerCheck
+    # manual fix to blank out this one protein, to see the entry
+    hgsql -e 'select * from ncbiRefSeqLink where protAcc="NP_989875.1";' rheMac10
+    hgsql -e 'update ncbiRefSeqLink set protAcc="" where protAcc="NP_989875.1";' rheMac10
+    # this makes the 'protein' link disappear from the gene details page
+    # curious that this gene is marked as a non-coding gene anyway ?
+    # gene: FET1 at chr4:63,102,774-63,105,516-
+
+    featureBits -enrichment rheMac10 refGene ncbiRefSeq 
+ # refGene 1.374%, ncbiRefSeq 8.397%, both 1.370%, cover 99.73%, enrich 11.88x
+    featureBits -enrichment rheMac10 ncbiRefSeq refGene
+ # ncbiRefSeq 8.397%, refGene 1.374%, both 1.370%, cover 16.32%, enrich 11.88x
+
+    featureBits -enrichment rheMac10 ncbiRefSeqCurated refGene
+ # ncbiRefSeqCurated 1.368%, refGene 1.374%, both 1.364%, cover 99.71%, enrich 72.59x
+    featureBits -enrichment rheMac10 refGene ncbiRefSeqCurated
+ # refGene 1.374%, ncbiRefSeqCurated 1.368%, both 1.364%, cover 99.32%, enrich 72.59x
+
+#########################################################################
+# LIFTOVER TO rheMac8 (DONE - 2019-07-02 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02
+    cd /hive/data/genomes/rheMac10/bed/blat.rheMac8.2019-07-02
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \
+         rheMac10 rheMac8
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -ooc=/hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc \
+         rheMac10 rheMac8) > doLiftOverToRheMac8.log 2>&1
+XXX - running - Tue Jul  2 08:11:05 PDT 2019
+    # real    156m30.215s
+
+    # see if the liftOver menus function in the browser from rheMac10 to galGal5
+
+#########################################################################
+#  BLATSERVERS ENTRY (TBD - 2018-10-12 - Hiram)
+#	After getting a blat server assigned by the Blat Server Gods,
+    ssh hgwdev
+
+    hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+	VALUES ("rheMac10", "blat1a", "17892", "1", "0"); \
+	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
+	VALUES ("rheMac10", "blat1a", "17893", "0", "1");' \
+	    hgcentraltest
+    #	test it with some sequence
+
+############################################################################
+## reset default position to MEPE gene (egg shell protein)
+##  (TBD - 2018-10-12 - Hiram)
+
+    # as found from the galGal5 to rheMac10 liftOver
+    ssh hgwdev
+    hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928"
+	where name="rheMac10";' hgcentraltest
+
+#########################################################################
+# crispr 10K shoulders (TBD - 2018-10-16 - Hiram)
+    # working on this script, adding the indexFa step:
+    time (~/kent/src/hg/utils/automation/doCrispr.pl \
+	-stop=indexFa -buildDir=`pwd` -smallClusterHub=ku rheMac10 ncbiRefSeq) \
+	> indexFa.log 2>&1
+    # real    23m26.694s
+
+    time (~/kent/src/hg/utils/automation/doCrispr.pl \
+       -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \
+           rheMac10 ncbiRefSeq) > guides.log 2>&1
+    # real    2m50.758s
+
+    # adding the /dev/shm/ setup rsync for the indexed Fa
+    # performed manually to work out the procedure
+    time (~/kent/src/hg/utils/automation/doCrispr.pl \
+        -continue=specScores -stop=specScores -buildDir=`pwd` \
+           -smallClusterHub=ku rheMac10 ncbiRefSeq) > specScores.log
+
+    # had about half of ku for about half this time:
+# Completed: 884922 of 884922 jobs
+# CPU time in finished jobs:  35872791s  597879.85m  9964.66h  415.19d  1.138 y
+# IO & Wait Time:               899261s   14987.69m   249.79h   10.41d  0.029 y
+# Average job time:                 42s       0.69m     0.01h    0.00d
+# Longest finished job:             88s       1.47m     0.02h    0.00d
+# Submission to last job:        48045s     800.75m    13.35h    0.56d
+
+
+    time find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab
+    # real    236m17.220s
+    wc -l specScores.tab
+    # 66451712 specScores.tab
+
+    time (~/kent/src/hg/utils/automation/doCrispr.pl \
+	-continue=effScores -stop=load \
+	    -buildDir=`pwd` -smallClusterHub=ku rheMac10 ncbiRefSeq) \
+	> load.log
+    # real    307m41.143s
+
+#########################################################################
+# all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram)
+xyz
+    cd $HOME/kent/src/hg/makeDb/schema
+    # verify all the business is done for release
+    ~/kent/src/hg/utils/automation/verifyBrowser.pl rheMac10
+
+    # fixup all.joiner until this is a clean output
+    joinerCheck -database=rheMac10 -tableCoverage all.joiner
+    joinerCheck -database=rheMac10 -times all.joiner
+    joinerCheck -database=rheMac10 -keys all.joiner
+
+    # when clean, check in:
+    git commit -m 'adding rules for rheMac10 refs #22113' all.joiner
+    git push
+    # run up a 'make alpha' in hg/hgTables to get this all.joiner file
+    # into the hgwdev/genome-test system
+
+    cd /hive/data/genomes/rheMac10
+    time (makeDownloads.pl rheMac10) > downloads.log 2>&1
+    #  real    10m7.605s
+
+    #   now ready for pushQ entry
+    mkdir /hive/data/genomes/rheMac10/pushQ
+    cd /hive/data/genomes/rheMac10/pushQ
+  time (makePushQSql.pl -redmineList rheMac10) > rheMac10.pushQ.sql 2> stderr.out
+    # real    9m58.779s
+
+    # remove the extra chainNet files from the listings:
+    sed -i -e "/etNig1/d" redmine.rheMac10.file.list
+    sed -i -e "/asAcu1/d" redmine.rheMac10.file.list
+    sed -i -e "/etNig1/d" redmine.rheMac10.table.list
+    sed -i -e "/onAlb1/d" redmine.rheMac10.table.list
+    sed -i -e "/asAcu1/d" redmine.rheMac10.table.list
+    sed -i -e "/Stickleback/d" redmine.rheMac10.releaseLog.txt
+    sed -i -e "/Tetraodon/d" redmine.rheMac10.releaseLog.txt
+    sed -i -e "/sparrow/d" redmine.rheMac10.releaseLog.txt
+    # remove the tandemDups and gapOverlap from the file list:
+    sed -i -e "/tandemDups/d" redmine.rheMac10.table.list
+    sed -i -e "/Tandem Dups/d" redmine.rheMac10.releaseLog.txt
+    sed -i -e "/gapOverlap/d" redmine.rheMac10.table.list
+    sed -i -e "/Gap Overlaps/d" redmine.rheMac10.releaseLog.txt
+    #  real    7m21.629s
+
+    #   check for errors in stderr.out, some are OK, e.g.:
+    # WARNING: hgwdev does not have /gbdb/rheMac10/wib/gc5Base.wib
+    # WARNING: hgwdev does not have /gbdb/rheMac10/wib/quality.wib
+    # WARNING: hgwdev does not have /gbdb/rheMac10/bbi/quality.bw
+    # WARNING: rheMac10 does not have seq
+    # WARNING: rheMac10 does not have extFile
+
+    # add the path names to the listing files in the redmine issue
+    # in the three appropriate entry boxes:
+
+#	/hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.file.list
+#	/hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.releaseLog.txt
+#	/hive/data/genomes/rheMac10/pushQ/redmine.rheMac10.table.list
+
+#########################################################################