src/hg/makeDb/doc/felCatV17e.txt 1.9
1.9 2010/04/27 19:20:00 chinhli
Add multiz 6 ways support
Index: src/hg/makeDb/doc/felCatV17e.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/felCatV17e.txt,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/hg/makeDb/doc/felCatV17e.txt 9 Apr 2010 18:41:24 -0000 1.8
+++ src/hg/makeDb/doc/felCatV17e.txt 27 Apr 2010 19:20:00 -0000 1.9
@@ -1,720 +1,845 @@
# for emacs: -*- mode: sh; -*-
# $Id$
# Felis Catus (domestic cat) -- NHGRI/GTB V17e/felCatV17e (2009-05-25)
# file template copied from calJac3.txt
# Felis catus (Project ID: 32759) by NHGRI/Genome Technology Branch [Draft
# assembly] sequence:
# ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/
# Felis_catus/catChrV17e
# Felis catus
##########################################################################
# Download sequence (DONE - 2010-03-03 Chin)
mkdir /hive/data/genomes/felCatV17e
cd /hive/data/genomes/felCatV17e
mkdir genbank
cd genbank
wget --timestamping -r --cut-dirs=6 --level=0 -nH -x \
--no-remove-listing -np \
"ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Felis_catus/catChrV17e/*"
# FINISHED --09:05:15--
# Downloaded: 151 files, 1.3G in 7m 42s (2.98 MB/s)
# Read ASSEMBLY_INFO
mkdir ucscChr
# stay at genbank directory
# fixup the accession names to become UCSC chrom names
S=Primary_Assembly/assembled_chromosomes
cut -f1 ${S}/chr2acc | while read C
do
ACC=`grep "${C}" ${S}/chr2acc | cut -f2`
echo "${ACC} -> chr${C}"
zcat ${S}/AGP/chr${C}.agp.gz \
| sed -e "s/^${ACC}/chr${C}/" | gzip > ucscChr/chr${C}.agp.gz
done
# use component instead
S=Primary_Assembly/assembled_chromosomes
cut -f1 ${S}/chr2acc | while read C
do
ACC=`grep "${C}" ${S}/chr2acc | cut -f2`
echo "${ACC} -> chr${C}"
zcat ${S}/AGP/chr${C}.comp.agp.gz \
| sed -e "s/^${ACC}/chr${C}/" | gzip > ucscChr/chr${C}.comp.agp.gz
done
S=Primary_Assembly/assembled_chromosomes
cut -f1 ${S}/chr2acc | while read C
do
ACC=`grep "${C}" ${S}/chr2acc | cut -f2`
echo "${ACC} -> chr${C}"
echo ">chr${C}" > ucscChr/chr${C}.fa
zcat ${S}/FASTA/chr${C}.fa.gz | grep -v "^>" >> ucscChr/chr${C}.fa
gzip ucscChr/chr${C}.fa &
done
# Check them with faSize
faSize Primary_Assembly/assembled_chromosomes/FASTA/chr*.fa.gz
# 2872644707 bases (1165972091 N's 1706672616 real 1706672616 upper 0
# lower) in 19 sequences in 19 files
faSize ucscChr/chr*.fa.gz
# 2872644707 bases (1165972091 N's 1706672616 real 1706672616 upper 0
# lower) in 19 sequences in 19 files
# For unplaced scalfolds, named them as chrUn_xxxxxxxx
# where xxxxxx is the original access id as: chrUn_ACBE01000381.1
# and put it into chrUn.* files
# copy all the comment lines (start with #)
S=Primary_Assembly/unplaced_scaffolds
zcat ${S}/AGP/unplaced.scaf.agp.gz | grep "^#" > ucscChr/chrUn.agp
# append the gap records
zcat ${S}/AGP/unplaced.scaf.agp.gz | grep -v "^#" \
| sed -e "s/^/chrUn_/" >> ucscChr/chrUn.agp
gzip ucscChr/chrUn.agp &
zcat ${S}/FASTA/unplaced.scaf.fa.gz \
| sed -e "s#^>.*|gb|#>chrUn_#; s#|.*##" | gzip > ucscChr/chrUn.fa.gz
# about 104034 sequences in the unplaced
zcat ucscChr/chrUn.fa.gz | grep "^>" | wc
# 104034 104034 2275648
# Check them with faSize
faSize Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz
# 287642232 bases (3696852 N's 283945380 real 283945380 upper 0
# lower) in 104034 sequences in 1 files
faSize ucscChr/chrUn.fa.gz
# 287642232 bases (3696852 N's 283945380 real 283945380 upper 0
# lower) in 104034 sequences in 1 files
##########################################################################
# Initial genome build (Done - 2010-03-03 -Chin)
# decide the right order by
hgsql -e "select orderKey,name from dbDb order by orderKey;" \
hgcentraltest | less
# 168 cavPor3
# 169 cavPor2
# 189 oryCun2
# 190 oryCun1
# 191 ochPri2
# 200 eriEur1
# 217 felCat3
cd /hive/data/genomes/felCatV17e
cat << '_EOF_' > felCatV17e.config.ra
# Config parameters for makeGenomeDb.pl:
db felCatV17e
clade mammal
genomeCladePriority 16
scientificName Felis catus
commonName Cat
assemblyDate Dec. 2008
assemblyLabel NHGRI/Genome Technology Branch (NCBI project 10703, accession ACBE0100000)
assemblyShortLabel NHGRI/GTB V17e
orderKey 216
mitoAcc NC_001700
fastaFiles /hive/data/genomes/felCatV17e/genbank/ucscChr/chr*.fa.gz
agpFiles /hive/data/genomes/felCatV17e/genbank/ucscChr/chr*.agp.gz
# qualFiles none
dbDbSpeciesDir cat
taxId 9685
'_EOF_'
makeGenomeDb.pl -stop seq felCatV17e.config.ra > seq.log 2>&1 &
time makeGenomeDb.pl -continue=agp -stop=agp felCatV17e.config.ra > agp.log 2>&1 &
# real 0m50.486s
time makeGenomeDb.pl -continue=db -stop=db felCatV17e.config.ra > db.log 2>&1 &
#real 7m50.591s
time makeGenomeDb.pl -continue=dbDb -stop=dbDb felCatV17e.config.ra > dbDb.log 2>&1 &
time makeGenomeDb.pl -continue=trackDb felCatV17e.config.ra > trackDb.log 2>&1 &
#### 03/15 fixing the agp using the component one
# manually run hgLoadGapGl (as in jkStuff/makeDb.csh)
# without rerun the makeGenomeDb -continue=gap step
zcat genbank/ucscChr/chr*.comp.agp.gz | grep -v '^#' \
| sort -k1,1 -k2n,2n > felCatV17e.comp.agp
zcat genbank/ucscChr/chrUn.agp.gz | grep -v '^#' >> felCatV17e.comp.agp
grep chrM felCatV17e.agp >> felCatV17e.comp.agp
checkAgpAndFa felCatV17e.comp.agp felCatV17e.unmasked.2bit
# loop: chrM, dnaOffset=0, seqSize=17009
# chrM 1 17009 230 F NC_001700 1 17009 +
# agpFrag->chromStart: 0, agpFrag->chromEnd: 17009, dnaOffset: 0
# FASTA sequence entry
# valid Fasta file entry
# all AGP and FASTA entries agree - both files are valid
dbSnoop felCatV17e before.txt
hgGoldGapGl -noGl felCatV17e felCatV17e.comp.agp
dbSnoop felCatV17e after.txt
diff before.txt after.txt # to see the change of rows in gold and gap tables
# > 35,861,584 gold 506,133 24,249,424 11,612,160
# > 28,192,744 gap 500,507 22,068,200 6,124,544
# 26,27d27
# < 858,728 gold 9,961 539,240 319,488
# < 345,208 gap 4,335 236,664 108,544
featureBits -countGaps felCatV17e gap
# 1169658726 bases of 3160303948 (37.011%) in intersection
hgsql -e "select type from gap;" felCatV17e | sort | uniq -c
# 381 contig
# 500126 fragment
# 1 type
mv felCatV17e.comp.agp felCatV17e.agp
##########################################################################
# fixed up the html files (working - 2010-04-06 Chin)
# per instructions at end of makeGenomeDb.log, edit the html file
# and checkin the *.ra and *.html files.
cd /cluster/home/chinhli/kent/src/hg/makeDb/trackDb/cat/felCatV17e
##########################################################################
# running repeat masker (DONE - 2010-03-05 - Chin)
mkdir /hive/data/genomes/felCatV17e/bed/repeatMasker
cd /hive/data/genomes/felCatV17e/bed/repeatMasker
time doRepeatMasker.pl -buildDir=`pwd` -noSplit \
-bigClusterHub=swarm -dbHost=hgwdev -workhorse=hgwdev \
-smallClusterHub=encodek felCatV17e > do.log 2>&1 &
# real 530m25.613s
cat faSize.rmsk.txt
# 3160303948 bases (1169668943 N's 1990635005 real 1183631401
# upper 807003604 lower) in 104054 sequences in 1 files
# %25.54 masked total, %40.54 masked real
##########################################################################
# running simple repeat (DONE - 2010-03-16 Chin)
mkdir /hive/data/genomes/felCatV17e/bed/simpleRepeat
cd /hive/data/genomes/felCatV17e/bed/simpleRepeat
time doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=swarm \
-dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=encodek \
felCatV17e > do.log 2>&1 &
# reall 149m19.948s
cat fb.simpleRepeat
# 49107705 bases of 2690950627 (1.825%) in intersection
cd /hive/data/genomes/felCatV17e
twoBitMask felCatV17e.rmsk.2bit \
-add bed/simpleRepeat/trfMask.bed felCatV17e.2bit
# you can safely ignore the warning about fields >= 13
twoBitToFa felCatV17e.2bit stdout | faSize stdin > faSize.felCatV17e.2bit.txt
cat faSize.felCatV17e.2bit.txt
# 3160303948 bases (1169668943 N's 1990635005 real 1182766163 upper
# 807868842 lower) in 104054 sequences in 1 files
# %25.56 masked total, %40.58 masked real
# double check with featureBits
featureBits -countGaps felCatV17e gap
# 1169668943 bases of 3160303948 (37.011%) in intersection
rm /gbdb/felCatV17e/felCatV17e.2bit
ln -s `pwd`/felCatV17e.2bit /gbdb/felCatV17e/felCatV17e.2bit
########################################################################
# Marking *all* gaps - they are not all in the AGP file
# (DONE - 2010-03-16 - Chin)
mkdir /hive/data/genomes/felCatV17e/bed/allGaps
cd /hive/data/genomes/felCatV17e/bed/allGaps
time nice -n +19 findMotif -motif=gattaca -verbose=4 \
-strand=+ ../../felCatV17e.rmsk.2bit > findMotif.txt 2>&1
# real 1m45.351s
grep "^#GAP " findMotif.txt | sed -e "s/^#GAP //" > allGaps.bed
featureBits felCatV17e -not gap -bed=notGap.bed
# 1990645222 bases of 1990645222 (100.000%) in intersection
featureBits felCatV17e allGaps.bed notGap.bed -bed=new.gaps.bed
# 10217 bases of 1990645222 (0.001%) in intersection
# (real time 7+ hours)
# what is the last index in the existing gap table:
hgsql -N -e "select ix from gap;" felCatV17e | sort -n | tail -1
# 101050
cat << '_EOF_' > mkGap.pl
#!/usr/bin/env perl
use strict;
use warnings;
my $ix=`hgsql -N -e "select ix from gap;" felCatV17e | sort -n | tail -1`;
chomp $ix;
open (FH,"<new.gaps.bed") or die "can not read new.gaps.bed";
while (my $line = <FH>) {
my ($chrom, $chromStart, $chromEnd, $rest) = split('\s+', $line);
++$ix;
printf "%s\t%d\t%d\t%d\tN\t%d\tother\tyes\n", $chrom, $chromStart,
$chromEnd, $ix, $chromEnd-$chromStart;
}
close (FH);
'_EOF_'
# << happy emacs
chmod +x ./mkGap.pl
./mkGap.pl > other.gap
hgLoadBed -sqlTable=$HOME/kent/src/hg/lib/gap.sql \
-noLoad felCatV17e otherGap other.gap
# Reading other.gap
# Loaded 1294 elements of size 8
# Sorted
# Saving bed.tab
# No load option selected, see file: bed.tab
wc -l bed.tab
# 1294 bed.tab
# starting with this many
hgsql -e "select count(*) from gap;" felCatV17e
# 500507
hgsql felCatV17e -e 'load data local infile "bed.tab" into table gap;'
# result count:
hgsql -e "select count(*) from gap;" felCatV17e
# 501801
# == 500507 + 1294
#########################################################################
# MAKE 11.OOC FILES FOR BLAT (DONE - 2010-02-03 - Chin)
cat faSize.felCatV17e.2bit.txt
# 3160303948 bases (1169668943 N's 1990635005 real 1182766163 upper
# 807868842 lower) in 104054 sequences in 1 files
# %25.56 masked total, %40.58 masked real
# numerator is felCatV17e gapless bases "real" as reported by faSize
# denominator is hg17 gapless bases as reported by featureBits,
# 1024 is threshold used for human -repMatch:
calc \( 1990635005 / 2897310462 \) \* 1024
# ( 1990635005 / 2897310462 ) * 1024 = 703.552578
# ==> use -repMatch=700 according to size scaled down from 1024 for human.
# and rounded down to nearest 50
cd /hive/data/genomes/felCatV17e
blat felCatV17e.2bit /dev/null /dev/null -tileSize=11 \
-makeOoc=jkStuff/felCatV17e.11.ooc -repMatch=700
# Wrote 23033 overused 11-mers to jkStuff/felCatV17e.11.ooc
mkdir /hive/data/staging/data/felCatV17e
cp -p felCatV17e.2bit chrom.sizes jkStuff/felCatV17e.11.ooc \
/hive/data/staging/data/felCatV17e
gapToLift -bedFile=jkStuff/nonBridgedGaps.bed felCatV17e \
jkStuff/felCatV17e.nonBridged.lft
# Ask the admin to copy the
# /hive/data/staging/data/felCatV17e directory
# to cluster nodes: /scratch/data/felCatV17e
##########################################################################
# BLATSERVERS ENTRY (DONE - 2009-12-23 - Chin)
# After getting a blat server assigned by the Blat Server Gods,
#
hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
VALUES ("felCatV17e", "blat4", "17778", "1", "0"); \
INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
VALUES ("felCatV17e", "blat4", "17779", "0", "1");' \
hgcentraltest
# test it with some sequence
############################################################################
# chrA2:64650765-64656835
# reset position to RHO location as found from blat of hg19 RHO gene
hgsql -e \
'update dbDb set defaultPos="chrA2:64650765-64656835" where
name="felCatV17e";' \
hgcentraltest
############################################################################
# genbank run DONE - 2010-03-16 - Chin )
ssh hgwdev
cd $HOME/kent/src/hg/makeDb/genbank
# edit etc/genbank.conf to add this section just before calJac1:
# Marmoset
felCatV17e.serverGenome = /hive/data/genomes/felCatV17e/felCatV17e.2bit
felCatV17e.clusterGenome = /scratch/data/felCatV17e/felCatV17e.2bit
felCatV17e.ooc = /scratch/data/felCatV17e/felCatV17e.11.ooc
felCatV17e.lift = no
felCatV17e.perChromTables = no
felCatV17e.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter}
felCatV17e.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
felCatV17e.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
felCatV17e.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
felCatV17e.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter}
felCatV17e.genbank.est.xeno.pslCDnaFilter = ${ordered.genbank.est.xeno.pslCDnaFilter}
felCatV17e.downloadDir = felCatV17e
felCatV17e.refseq.mrna.native.load = yes
felCatV17e.refseq.mrna.xeno.load = yes
felCatV17e.refseq.mrna.xeno.loadDesc = yes
cvs ci -m "adding felCatV17e" etc/genbank.conf
make etc-update
ssh genbank
screen # control this business with a screen since it takes a while
cd /cluster/data/genbank
time nice -n +19 bin/gbAlignStep -initial felCatV17e &
# tail var/build/logs/2010.03.17-10:43:18.felCatV17e.initalign.log
# gbAlignInstall: complete: real=3.63
# genbank 2010.03.17-16:33:21 felCatV17e.initalign: finish
ssh hgwdev
cd /cluster/data/genbank
time ./bin/gbDbLoadStep -drop -initialLoad felCatV17e &
# logFile:
# tail var/dbload/hgwdev/logs/2010.03.18-15:03:58.dbload.log
# real 31m56.710s
# enable daily alignment and update of hgwdev
cd ~/kent/src/hg/makeDb/genbank
cvsup
# add felCatV17e to:
etc/align.dbs
etc/hgwdev.dbs
cvs ci -m "Adding felCatV17e - Cat - Felis catus" \
etc/align.dbs etc/hgwdev.dbs
make etc-update
# DONE - 2010-03-17 - Chin
############################################################################
# running cpgIsland business (DONE - 2010-03-17 - Chin)
mkdir /hive/data/genomes/felCatV17e/bed/cpgIsland
cd /hive/data/genomes/felCatV17e/bed/cpgIsland
cvs -d /projects/compbio/cvsroot checkout -P hg3rdParty/cpgIslands
cd hg3rdParty/cpgIslands
# needed to fixup this source, adding include to readseq.c:
#include "string.h"
# and to cpg_lh.c:
#include "unistd.h"
#include "stdlib.h"
# and fixing a declaration in cpg_lh.c
sed -e "s#\(extern char\* malloc\)#// \1#" cpg_lh.c > tmp.c
mv tmp.c cpg_lh.c
make
cd ../../
ln -s hg3rdParty/cpgIslands/cpglh.exe
mkdir -p hardMaskedFa
cut -f1 ../../chrom.sizes | while read C
do
echo ${C}
twoBitToFa ../../felCatV17e.2bit:$C stdout \
| maskOutFa stdin hard hardMaskedFa/${C}.fa
done
ssh swarm
cd /hive/data/genomes/felCatV17e/bed/cpgIsland
mkdir results
cut -f1 ../../chrom.sizes > chr.list
cat << '_EOF_' > template
#LOOP
./runOne $(path1) {check out exists results/$(path1).cpg}
#ENDLOOP
'_EOF_'
# << happy emacs
# the faCount business is to make sure there is enough sequence to
# work with in the fasta. cpglh.exe does not like files with too many
# N's - it gets stuck
cat << '_EOF_' > runOne
#!/bin/csh -fe
set C = `faCount hardMaskedFa/$1.fa | grep ^chr | awk '{print $2 - $7 }'`
if ( $C > 200 ) then
./cpglh.exe hardMaskedFa/$1.fa > /scratch/tmp/$1.$$
mv /scratch/tmp/$1.$$ $2
else
touch $2
endif
'_EOF_'
# << happy emacs
gensub2 chr.list single template jobList
para create jobList
para try
para check ... etc
para time
# in jobList:
# .....
# ./runOne chrD3 {check out exists results/chrD3.cpg}
# wc -l jobList
# .....
# 104054 jobList
# Completed: 104054 of 104054 jobs
# CPU time in finished jobs: 214s 3.57m 0.06h 0.00d 0.000 y
# IO & Wait Time: 935922s 15598.69m 259.98h 10.83d 0.030 y
# Average job time: 9s 0.15m 0.00h 0.00d
# Longest finished job: 174s 2.90m 0.05h 0.00d
# Submission to last job: 1136s 18.93m 0.32h 0.01d
# Transform cpglh output to bed +
catDir results | awk '{
$2 = $2 - 1;
width = $3 - $2;
printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n",
$1, $2, $3, $5,$6, width,
$6, width*$7*0.01, 100.0*2*$6/width, $7, $9);
}' > cpgIsland.bed
cd /hive/data/genomes/felCatV17e/bed/cpgIsland
hgLoadBed felCatV17e cpgIslandExt -tab \
-sqlTable=$HOME/kent/src/hg/lib/cpgIslandExt.sql cpgIsland.bed
# Reading cpgIsland.bed
# Loaded 57950 elements of size 10
# Sorted
# Creating table definition for cpgIslandExt
# Saving bed.tab
# Loading felCatV17e
# check it with featureBits felCatV17e cpgIslandExt
# 36646772 bases of 1990635005 (1.841%) in intersection
# cleanup
rm -fr hardMaskedFa
#######################################################################
# felCatV17e Cat BLASTZ/CHAIN/NET (DONE - 2010-03-22 - Chin)
screen # use a screen to manage this multi-day job
mkdir /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
cd /hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
cat << '_EOF_' > DEF
# dog vs. cat
# maximum M allowed with lastz is only 254
BLASTZ_M=254
# TARGET: Dog canFan2
SEQ1_DIR=/scratch/data/canFam2/canFam2.2bit
SEQ1_LEN=/scratch/data/canFam2/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
SEQ1_LIMIT=5
# QUERY: Cat (felCatV17e)
SEQ2_DIR=/scratch/data/felCatV17e/felCatV17e.2bit
SEQ2_LEN=/scratch/data/felCatV17e/chrom.sizes
SEQ2_LIMIT=50
SEQ2_CHUNK=10000000
SEQ2_LAP=0
BASE=/hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22
TMPDIR=/scratch/tmp
'_EOF_'
# << this line keeps emacs coloring happy
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-syntenicNet -noDbNameCheck \
-chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> do.log 2>&1 &
# real 287m24.258s
cat fb.canFam2.chainFelCatV17eLink.txt
# 1481040604 bases of 2384996543 (62.098%) in intersection
mkdir /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.canFam2.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/canFam2/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 251m14.341s
# *** All done ! Elapsed time: 251m14s
# *** Make sure that goldenPath/felCatV17e/vsCanFam2/README.txt is
# accurate.
# *** Add {chain,net}CanFam2 tracks to trackDb.ra if necessary.
cat fb.felCatV17e.chainCanFam2Link.txt
# 1467506008 bases of 1990635005 (73.720%) in intersection
#####################################################################
# LASTZ Mouse Swap (DONE - 2010-03-22 - Chin)
cd /hive/data/genomes/mm9/bed/lastzFelCatV17e.2010-03-22
cat fb.mm9.chainFelCatV17eLink.txt
# 637007193 bases of 2620346127 (24.310%) in intersection
# swap
mkdir /hive/data/genomes/felCatV17e/bed/blastz.mm9.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.mm9.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/mm9/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 125m37.926s
cat fb.felCatV17e.chainMm9Link.txt
# 616529959 bases of 1990635005 (30.972%) in intersection
#####################################################################
# LASTZ Human Swap (DONE - 2010-03-22 - Chin)
cd /hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22
cat fb.hg19.chainFelCatV17eLink.txt
# 1266003011 bases of 2897316137 (43.696%) in intersection
# Swap re-run 04-07
mkdir /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/hg19/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
-workhorse=hgwdev -smallClusterHub=pk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 200m43.245s
cat fb.felCatV17e.chainHg19Link.txt
# 1211702270 bases of 1990635005 (60.870%) in intersection
#####################################################################
# LASTZ Panda Swap (DONE - 2010-03-22 - Chin)
cd /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22
cat fb.felCatV17e.chainAilMel1Link.txt
# 1503647735 bases of 1990635005 (75.536%) in intersection
+ # re-run swap 04-26
mkdir /hive/data/genomes/felCatV17e/bed/blastz.ailMel1.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.ailMel1.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 155m57.566s
+ cd /hive/data/genomes/ailMel1/bed/blastz.felCatV17e.swap
cat fb.ailMel1.chainFelCatV17eLink.txt
# 1507273252 bases of 2245312831 (67.130%) in intersection
-
-
+ # Due to the SEQ1 and SEQ2 spec'ed in
+ # /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22/DEF
+ # need to copy the swap directory from ailMel1 to felCatv17e
+ # also need to rename from ailMel1.felCatV17e, or 6way step will have
+ # problem
+ # Ping hiram for this
#####################################################################
# LASTZ Oppsom Swap (DONE - 2010-03-22 - Chin)
cd /hive/data/genomes/monDom5/bed/lastzFelCatV17e.2010-03-22
cat fb.monDom5.chainFelCatV17eLink.txt
# 178616721 bases of 3501660299 (5.101%) in intersection
# Swap
mkdir /hive/data/genomes/felCatV17e/bed/blastz.monDom5.swap
cd /hive/data/genomes/felCatV17e/bed/blastz.monDom5.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/monDom5/bed/lastzFelCatV17e.2010-03-22/DEF \
-swap -syntenicNet -noDbNameCheck \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
-chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
# *** All done ! Elapsed time: 100m29s
# *** Make sure that goldenPath/felCatV17e/vsMonDom5/README.txt is
# accurate.
# *** Add {chain,net}MonDom5 tracks to trackDb.ra if necessary.
cat fb.felCatV17e.chainMonDom5Link.txt
# 166499264 bases of 1990635005 (8.364%) in intersection
############################################################################
# ctgPos2 track - showing clone sequence locations on chromosomes
# (DONE - 2010-03-30 - Chin)
mkdir /hive/data/genomes/felCatV17e/bed/ctgPos2
cd /hive/data/genomes/felCatV17e/bed/ctgPos2
cat << '_EOF_' > agpToCtgPos2.pl
#!/usr/bin/env perl
use warnings;
use strict;
my $argc = scalar(@ARGV);
if ($argc != 1) {
printf STDERR "usage: zcat your.files.agp.gz | agpToCtgPos2.pl
/dev/stdin > ctgPos2.tab\n";
exit 255;
}
my $agpFile = shift;
open (FH, "<$agpFile") or die "can not read $agpFile";
while (my $line = <FH>) {
next if ($line =~ m/^#/);
chomp $line;
my @a = split('\s+', $line);
next if ($a[4] =~ m/^N$/);
next if ($a[4] =~ m/^U$/);
my $chrSize = $a[2]-$a[1]+1;
my $ctgSize = $a[7]-$a[6]+1;
die "sizes differ $chrSize != $ctgSize\n$line\n" if ($chrSize !=
$ctgSize);
printf "%s\t%d\t%s\t%d\t%d\t%s\n", $a[5], $chrSize, $a[0], $a[1]-1,
$a[2], $a[4];
}
close (FH);
'_EOF_'
# << happy emacs
chmod 775 agpToCtgPos2.pl
export S=../../genbank/Primary_Assembly/assembled_chromosomes
cut -f2 ${S}/chr2acc | while read ACC
do
C=`grep "${ACC}" ${S}/chr2acc | cut -f1`
zcat ${S}/AGP/chr${C}.agp.gz \
| sed -e "s/^${ACC}/chr${C}/"
done | ./agpToCtgPos2.pl /dev/stdin > ctgPos2.tab
hgLoadSqlTab felCatV17e ctgPos2 $HOME/kent/src/hg/lib/ctgPos2.sql \
ctgPos2.tab
# add the track ctgPos2 to src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
# at src/makeDb/trackdb do "make update" or/and "make alpha"
#########################################################################
# all.joiner update, downloads and in pushQ - (DONE - 2010-04-09 Chin)
cd $HOME/kent/src/hg/makeDb/schema
# fixup all.joiner until this is a clean output
joinerCheck -database=felCatV17e -all all.joiner
mkdir /hive/data/genomes/felCatV17e/goldenPath
cd /hive/data/genomes/felCatV17e/goldenPath
makeDownloads.pl felCatV17e > do.log 2>&1
# vi /hive/data/genomes/felCatV17e/goldenPath/database/README.txt
# vi /hive/data/genomes/felCatV17e/goldenPath/bigZips/README.txt
# now ready for pushQ entry
mkdir /hive/data/genomes/felCatV17e/pushQ
cd /hive/data/genomes/felCatV17e/pushQ
makePushQSql.pl felCatV17e > felCatV17e.pushQ.sql 2> stderr.out
# check for errors in stderr.out, some are OK, e.g.:
# WARNING: felCatV17e does not have seq
# WARNING: felCatV17e does not have extFile
# WARNING: felCatV17e does not have tableDescriptions
# copy it to hgwbeta
# use hgcat in .hg.conf.beta
scp -p felCatV17e.pushQ.sql hgwbeta:/tmp
ssh hgwbeta
cd /tmp
hgsql qapushq < felCatV17e.pushQ.sql
# in that pushQ entry walk through each entry and see if the
# sizes will set properly
# reset to hguser in .hg.conf.beta
+#####################################################################
+## 6-Way Multiz (working - 2010-04-19 - Chin)
+# use /cluster/home/chinhli/kent/src/hg/utils/phyloTrees/49way.nh
+ mkdir /hive/data/genomes/felCatV17e/bed/multiz6way
+ cd /hive/data/genomes/felCatV17e/bed/multiz6way
+
+ /cluster/bin/phast/tree_doctor \
+ --prune-all-but=felCat3,hg19,mm9,canFam2,monDom5,ailMel1 \
+ --rename="felCat3 -> felCatV17e " \
+/cluster/home/chinhli/kent/src/hg/utils/phyloTrees/49way.nh > 6way.nh
+
+ # rearrange felCatV17e to the top, get some help from tree_doctor:
+ /cluster/bin/phast/tree_doctor --name-ancestors --reroot felCatV17e \
+ --with-branch 6way.nh
+ # edit out the ancestors, and move felCatV17e from the bottom to
+ # the top, resulting in this tree:
+
+(((felCatV17e:0.098612,(canFam2:0.052458,ailMel1:0.050000):0.050000):0.093470,(hg19:0.144018,mm9:0.356483):0.020593):0.258392,monDom5:0.340786);
+
+ # more rearranging after seeing what the distance table looks like
+ # below to get them appearing as much as possible in their
+ # distance order top to bottom: (TO_DO)
+
+ # use the phyloGif to get the tree image
+ /cluster/bin/x86_64/phyloGif -phyloGif_tree=6way.nh \
+ -phyloGif_width=260 -phyloGif_height=260 > 6way.gif
+
+ # more rearranging after seeing what the distance table looks like
+ # below to get them appearing as much as possible in their
+ # distance order top to bottom: (TO_DO)
+
+
+
+ # usee this specification in the phyloGif tool after changing the names:
+ /cluster/bin/phast/tree_doctor \
+--rename="felCatV17e -> Cat ; hg19 -> Human ; ailMel1 -> Panda ; canFam2 -> Dog ; mm9 -> Mouse ; monDom5 -> Opossum " 6way.nh
+
+ # http://genome.ucsc.edu/cgi-bin/phyloGif
+ # to obtain a gif image for htdocs/images/phylo/felCatV17e_6way.gif
+ /cluster/bin/x86_64/phyloGif -phyloGif_tree=6way.nh \
+ -phyloGif_width=260 -phyloGif_height=260 > felCatV17e_6way.gif
+
+ /cluster/bin/phast/all_dists 6way.nh > 6way.distances.txt
+ # make sure all symlinks lastz.DB -> lastzDb-date
+ # exist here and at the swap locations, the perl script expects this
+ # in order to find featureBits numbers.
+ cd /hive/data/genomes/felCatV17e/bed]
+ ln -s blastz.hg19.swap lastz.hg19
+ ln -s blastz.canFam2.swap lastz.canFam2
+ ln -s blastz.mm9.swap lastz.mm9
+ ln -s blastz.monDom5.swap lastz.monDom5
+ # ln -s blastz.ailMel1.swap lastz.ailMel1 (we switched SEQ1 and SEQ2)
+ ln -s /hive/data/genomes/ailMel1/bed/blastz.felCatV17e.swap lastz.ailMel1
+
+
+ cd /hive/data/genomes/felCatV17e/bed/multiz6way
+ # Use 6way.distances.txt to create the table below
+ # with this perl script:
+ cat << '_EOF_' > sizeStats.pl
+#!/usr/bin/env perl
+use strict;
+use warnings;
+
+
+open (FH, "grep -y felCatV17e 6way.distances.txt | sort -k3,3n|") or
+ die "can not read 6way.distances.txt";
+
+my $count = 0;
+while (my $line = <FH>) {
+ chomp $line;
+ my ($felCatV17e, $D, $dist) = split('\s+', $line);
+ my $chain = "chain" . ucfirst($D);
+ my $B="/hive/data/genomes/felCatV17e/bed/lastz.$D/fb.felCatV17e." .
+ $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.felCatV17e/fb.${D}.chainCalJac3Link.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;
+ ++$count;
+ if ($swapMeasure eq "N/A") {
+ printf "# %02d %.4f - %s %s\t(%% %.3f) (%s)\n", $count, $dist,
+ $orgName, $D, $chainLinkMeasure, $swapMeasure
+ } else {
+ printf "# %02d %.4f - %s %s\t(%% %.3f) (%% %.3f)\n", $count, $dist,
+ $orgName, $D, $chainLinkMeasure, $swapMeasure
+ }
+}
+close (FH);
+'_EOF_'
+ # << happy emacs
+ chmod +x ./sizeStats.pl
+ ./sizeStats.pl
+###### 04-27 stop here due to wrong output from sizeStats.pl
+###### pending move/rename aelMel1/felcatV17e lastz swap results
+# 02 0.1986 - Panda ailMel1 (% 0.000) (N/A)
+# 04 0.2011 - Dog canFam2 (% 73.720) (N/A)
+# 06 0.3567 - Human hg19 (% 60.870) (N/A)
+# 08 0.5692 - Mouse mm9 (% 30.972) (N/A)
+# 10 0.7913 - Opossum monDom5 (% 8.364) (N/A)
+
+
+
####################################################################