src/hg/makeDb/doc/ailMel1.txt 1.14
1.14 2010/04/30 21:17:30 chinhli
run doRecipBest.pl for felCatV17e
Index: src/hg/makeDb/doc/ailMel1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ailMel1.txt,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/hg/makeDb/doc/ailMel1.txt 20 Apr 2010 00:06:17 -0000 1.13
+++ src/hg/makeDb/doc/ailMel1.txt 30 Apr 2010 21:17:30 -0000 1.14
@@ -1,578 +1,583 @@
# for emacs: -*- mode: sh; -*-
# $Id$
# Panda sequence: http://panda.genomics.org.cn/page/panda/download.jsp
# Ailuropoda melanoleuca
##########################################################################
# Download sequence (DONE - 2009-12-17 - Hiram)
mkdir /hive/data/genomes/ailMel1
cd /hive/data/genomes/ailMel1
mkdir genbank
cd genbank
wget --timestamping -r --cut-dirs=6 --level=0 -nH -x \
--no-remove-listing -np \
"ftp.ncbi.nlm.nih.gov:genbank/genomes/Eukaryotes/vertebrates_mammals/Ailuropoda_melanoleuca/AilMel_1.0/*"
# first pass attempt at sequence from public.genomics.org.cn
# 2009-12-17
# NCBI has cleaned the sequence and removed a couple of scaffolds that
# are cloning vector sequence
mkdir download
cd download
wget --timestamping \
'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
wget --timestamping \
'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda_contig100.mapping_scaffolds_nucmer.list.clean.tab.sort.gff.gz'
wget --timestamping \
'ftp://panda.genomics.org.cn/pub/panda/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
faCount panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz > faCount.txt
grep "^scaff" faCount.txt | awk '{print $1}' > scaffold.list
faSomeRecords panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz \
scaffold.list stdout | gzip > scaffolds.fa.gz
hgFakeAgp scaffolds.fa.gz stdout | sed -e "s/D/W/" > fake.agp
##########################################################################
# Initial genome build (DONE - 2009-12-17 - Hiram)
cd /hive/data/genomes/ailMel1
cat << '_EOF_' > ailMel1.config.ra
# Config parameters for makeGenomeDb.pl:
db ailMel1
clade mammal
genomeCladePriority 19
scientificName Ailuropoda melanoleuca
commonName Panda
assemblyDate Dec. 2009
assemblyLabel BGI-Shenzhen AilMel 1.0 Dec. 2009
orderKey 220
mitoAcc NC_009492
fastaFiles /hive/data/genomes/ailMel1/genbank/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz
agpFiles /hive/data/genomes/ailMel1/genbank/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz
# qualFiles none
dbDbSpeciesDir panda
taxId 9646
makeGenomeDb.pl -workhorse=hgwdev -stop=seq ailMel1.config.ra > seq.out 2>&1
# real 4m4.783s
makeGenomeDb.pl -start=agp -stop=agp ailMel1.config.ra > agp.out 2>&1
# real 0m20.968s
makeGenomeDb.pl -start=db -stop=db ailMel1.config.ra > db.out 2>&1
# real 6m28.168s
makeGenomeDb.pl -start=dbDb -stop=dbDb ailMel1.config.ra > dbDb.out 2>&1
makeGenomeDb.pl -start=trackDb -stop=trackDb ailMel1.config.ra > trackDb.out 2>&1
##########################################################################
# running repeat masker (DONE - 2010-02-02 - Hiram)
mkdir /hive/data/genomes/ailMel1/bed/repeatMasker
cd /hive/data/genomes/ailMel1/bed/repeatMasker
doRepeatMasker.pl -buildDir=`pwd` -noSplit -bigClusterHub=swarm \
-workhorse=hgwdev ailMel1 > do.log 2>&1
cat faSize.rmsk.txt
# 2299509015 bases (54196184 N's 2245312831 real 1371210941 upper 874101890
# lower) in 81467 sequences in 1 files
# %38.01 masked total, %38.93 masked real
##########################################################################
# running simple repeat (DONE - 2010-02-02 - Hiram)
mkdir /hive/data/genomes/ailMel1/bed/simpleRepeat
cd /hive/data/genomes/ailMel1/bed/simpleRepeat
time doSimpleRepeat.pl -buildDir=`pwd` -smallClusterHub=swarm \
-workhorse=hgwdev ailMel1 > do.log 2>&1 &
# real 103m30.880s
cat fb.simpleRepeat
# 25064758 bases of 2245312831 (1.116%) in intersection
cd /hive/data/genomes/ailMel1
twoBitMask ailMel1.rmsk.2bit \
-add bed/simpleRepeat/trfMask.bed ailMel1.2bit
# you can safely ignore the warning about fields >= 13
twoBitToFa ailMel1.2bit stdout | faSize stdin > faSize.ailMel1.2bit.txt
cat faSize.ailMel1.2bit.txt
# 2299509015 bases (54196184 N's 2245312831 real 1370617891 upper
# 874694940 lower) in 81467 sequences in 1 files
# %38.04 masked total, %38.96 masked real
rm /gbdb/ailMel1/ailMel1.2bit
ln -s `pwd`/ailMel1.2bit /gbdb/ailMel1/ailMel1.2bit
##########################################################################
# BLATSERVERS ENTRY (DONE - 2009-12-23 - 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 ("ailMel1", "blat12", "17802", "1", "0"); \
INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
VALUES ("ailMel1", "blat12", "17803", "0", "1");' \
hgcentraltest
# test it with some sequence
#########################################################################
# MAKE 11.OOC FILES FOR BLAT (DONE - 2010-02-03 - Hiram)
ssh kolossus
# numerator is ailMel1 gapless bases as reported by faSize
# denominator is hg17 gapless bases as reported by featureBits,
# 1024 is threshold used for human -repMatch:
calc \( 2245312831 / 2897310462 \) \* 1024
# ( 2245312831 / 2897310462 ) * 1024 = 793.563675
# ==> use -repMatch=750 according to size scaled down from 1024 for human.
# and rounded down to nearest 50
cd /hive/data/genomes/ailMel1
blat ailMel1.2bit /dev/null /dev/null -tileSize=11 \
-makeOoc=jkStuff/ailMel1.11.ooc -repMatch=750
# Wrote 25467 overused 11-mers to jkStuff/ailMel1.11.ooc
mkdir /hive/data/staging/data/ailMel
cp -p ailMel1.2bit chrom.sizes jkStuff/ailMel1.11.ooc \
/hive/data/staging/data/ailMel1
#########################################################################
# genbank run (DONE - 2010-02-04 - Hiram)
ssh hgwdev
cd $HOME/kent/src/hg/makeDb/genbank
# edit etc/genbank.conf to add this section just after canFam2:
# ailMel1 (panda)
ailMel1.serverGenome = /hive/data/genomes/ailMel1/ailMel1.2bit
ailMel1.clusterGenome = /scratch/data/ailMel1/ailMel1.2bit
ailMel1.lift = no
ailMel1.ooc = /scratch/data/ailMel1/ailMel1.11.ooc
ailMel1.refseq.mrna.native.pslCDnaFilter = ${ordered.refseq.mrna.native.pslCDnaFilter}
ailMel1.refseq.mrna.xeno.pslCDnaFilter = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ailMel1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ailMel1.genbank.mrna.xeno.pslCDnaFilter = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ailMel1.genbank.est.native.pslCDnaFilter = ${ordered.genbank.est.native.pslCDnaFilter}
ailMel1.refseq.mrna.native.load = yes
ailMel1.refseq.mrna.xeno.load = yes
ailMel1.genbank.mrna.xeno.load = yes
ailMel1.downloadDir = ailMel1
ailMel1.perChromTables = no
# Edit src/lib/gbGenome.c to add new species. With these four lines:
# static char *ailMelNames[] = {"Ailuropoda melanoleuca", "Canis familiaris",
# "Canis sp.", "Canis lupus familiaris",
# "Canis lupus", NULL};
# ... later ...
# {"ailMel", ailMelNames},
cvs ci -m "adding ailMel - Panda with Dog specifications" src/lib/gbGenome.c
make install-server
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 ailMel1 &
# real 652m27.871s
# var/build/logs/2010.04.09-15:37:11.ailMel1.initalign.log
ssh hgwdev
cd /cluster/data/genbank
time ./bin/gbDbLoadStep -drop -initialLoad ailMel1 &
# logFile: var/dbload/hgwdev/logs/2010.04.12-10:13:40.dbload.log
# real 30m57.886s
# enable daily alignment and update of hgwdev
cd ~/kent/src/hg/makeDb/genbank
cvsup
# add oryCun2 to:
etc/align.dbs
etc/hgwdev.dbs
cvs ci -m "Adding ailMel1 - Panda - Ailuropoda melanoleuca" \
etc/align.dbs etc/hgwdev.dbs
make etc-update
# done - 2010-04-12 - Hiram
############################################################################
# reset position to RHO location as found from blat of hg19 RHO gene
hgsql -e \
'update dbDb set defaultPos="GL192818.1:558576-566855" where name="ailMel1";' \
hgcentraltest
############################################################################
# LASTZ Opossum monDom5 (DONE - 2010-02-05 - Hiram)
# original alignment
cd /hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04
cat fb.monDom5.chainAilMel1Link.txt
# 223510659 bases of 3501660299 (6.383%) in intersection
# and for the swap
mkdir /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
cd /hive/data/genomes/ailMel1/bed/blastz.monDom5.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/monDom5/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=5000 -chainLinearGap=loose > swap.log 2>&1 &
# real 69m35.464s
cat fb.ailMel1.chainMonDom5Link.txt
# 211209682 bases of 2245312831 (9.407%) in intersection
#########################################################################
# LASTZ Mouse Mm9 (DONE - 2010-02-05 - Hiram)
# original alignment
cd /hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04
cat fb.mm9.chainAilMel1Link.txt
# 749595031 bases of 2620346127 (28.607%) in intersection
# and for the swap
mkdir /hive/data/genomes/ailMel1/bed/blastz.mm9.swap
cd /hive/data/genomes/ailMel1/bed/blastz.mm9.swap
time doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/mm9/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -bigClusterHub=swarm -smallClusterHub=memk \
-workhorse=hgwdev \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 54m57.140s
cat fb.ailMel1.chainMm9Link.txt
# 739076250 bases of 2245312831 (32.916%) in intersection
#######################################################################
# felCatV17e Cat BLASTZ/CHAIN/NET (working - 2010-03-22 - Chin)
screen # use a screen to manage this multi-day job
mkdir /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22
cd /hive/data/genomes/ailMel1/bed/lastzFelCatV17e.2010-03-22
cat << '_EOF_' > DEF
# human vs. cat
# maximum M allowed with lastz is only 254
BLASTZ_M=254
# QUERY: Panda ailMel1
SEQ2_DIR=/scratch/data/ailMel1/ailMel1.2bit
SEQ2_LEN=/scratch/data/ailMel1/chrom.sizes
SEQ2_CHUNK=10000000
SEQ2_LAP=10000
SEQ2_LIMIT=300
# TARGET: Cat (felCatV17e)
SEQ1_DIR=/scratch/data/felCatV17e/felCatV17e.2bit
SEQ1_LEN=/scratch/data/felCatV17e/chrom.sizes
SEQ1_LIMIT=50
SEQ1_CHUNK=20000000
SEQ1_LAP=10000
BASE=/hive/data/genomes/ailMel1/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 &
# Command failed:
# doClusterRun.csh
# manually run the doClusterRun.csh 03/28
time ./doClusterRun.csh > doClusterRun.log 2>&1 &
# real 93m42.604s
# check with counting file number in psl directory to make sure that
# all jobs were completed.
# manually start with "cat" step
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
`pwd`/DEF \
-syntenicNet -continue=cat -noDbNameCheck \
-chainMinScore=3000 -chainLinearGap=medium \
-workhorse=hgwdev -smallClusterHub=encodek -bigClusterHub=swarm \
> cat.log 2>&1 &
# real 346m8.431s
cat fb.felCatV17e.chainAilMel1Link.txt
# 1503647735 bases of 1990635005 (75.536%) in intersection
+ # run rbest 2010-04-30
+ time doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
+ felCatV17e ailMel1 > rbest.log 2>&1 &
+ # real 234m49.556s
+
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
# need to change name back due to the seq1 and seq2 switch
# more TODO XXXX 03/29
# so should be able to do
# cat fb.felCatV17e.chainAilMel1Link.txt
# without
# cd /hive/data/genomes/ailMel1/bed/blastz.felCatV17e.swap
cat fb.ailMel1.chainFelCatV17eLink.txt
# 1507273252 bases of 2245312831 (67.130%) in intersection
#########################################################################
# all.joiner update, downloads and in pushQ - (DONE - 2010-04-01 - Hiram)
cd $HOME/kent/src/hg/makeDb/schema
# fixup all.joiner until this is a clean output
joinerCheck -database=ailMel1 -all all.joiner
mkdir /hive/data/genomes/ailMel1/goldenPath
cd /hive/data/genomes/ailMel1/goldenPath
makeDownloads.pl ailMel1 > do.log 2>&1
# now ready for pushQ entry
mkdir /hive/data/genomes/ailMel1/pushQ
cd /hive/data/genomes/ailMel1/pushQ
makePushQSql.pl ailMel1 > ailMel1.pushQ.sql 2> stderr.out
# check for errors in stderr.out, some are OK, e.g.:
# WARNING: ailMel1 does not have seq
# WARNING: ailMel1 does not have extFile
# WARNING: Could not tell (from trackDb, all.joiner and hardcoded lists of
# supporting and genbank tables) which tracks to assign these tables to:
# bosTau4ChainPileUp
# copy it to hgwbeta
scp -p ailMel1.pushQ.sql hgwbeta:/tmp
ssh hgwbeta
cd /tmp
hgsql qapushq < ailMel1.pushQ.sql
# in that pushQ entry walk through each entry and see if the
# sizes will set properly
############################################################################
# Marking *all* gaps - they are not all in the AGP file
# (DONE - 2010-03-25 - Hiram)
mkdir /hive/data/genomes/ailMel1/bed/allGaps
cd /hive/data/genomes/ailMel1/bed/allGaps
time nice -n +19 findMotif -motif=gattaca -verbose=4 \
-strand=+ ../../ailMel1.2bit > findMotif.txt 2>&1
# real 1m12.153s
grep "^#GAP " findMotif.txt | sed -e "s/^#GAP //" > allGaps.bed
featureBits ailMel1 -not gap -bed=notGap.bed
# 2245312831 bases of 2245312831 (100.000%) in intersection
featureBits ailMel1 allGaps.bed notGap.bed -bed=new.gaps.bed
# 0 bases of 2245312831 (0.000%) in intersection
# real 84m58.382s
# no new gaps
#########################################################################
# lastz Human hg19 swap (DONE - 2010-02-05 - Hiram)
# original alignment
cd /hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04
cat fb.hg19.chainAilMel1Link.txt
# 1453400264 bases of 2897316137 (50.164%) in intersection
# and the swap
mkdir /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
cd /hive/data/genomes/ailMel1/bed/blastz.hg19.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/hg19/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
real 124m14.393s
cat fb.ailMel1.chainHg19Link.txt
# 1411953704 bases of 2245312831 (62.884%) in intersection
#########################################################################
# lastz Dog canFam2 swap (DONE - 2010-02-05 - Hiram)
# original alignment
cd /hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04
cat fb.canFam2.chainAilMel1Link.txt
# 1791212709 bases of 2384996543 (75.103%) in intersection
# and the swap
mkdir /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
cd /hive/data/genomes/ailMel1/bed/blastz.canFam2.swap
time doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/canFam2/bed/lastzAilMel1.2010-02-04/DEF \
-swap -noLoadChainSplit -workhorse=hgwdev -bigClusterHub=pk \
-smallClusterHub=memk -chainMinScore=3000 -chainLinearGap=medium \
> swap.log 2>&1 &
# real 128m41.005s
cat fb.ailMel1.chainCanFam2Link.txt
# 1788107935 bases of 2245312831 (79.637%) in intersection
#########################################################################
# lastz Rat rn4 swap (DONE - 2010-02-18 - Hiram)
# original alignment
cd /hive/data/genomes/rn4/bed/lastzAilMel1.2010-02-04
cat fb.rn4.chainAilMel1Link.txt
# 708197812 bases of 2571531505 (27.540%) in intersection
# and the swap
mkdir /hive/data/genomes/ailMel1/bed/blastz.rn4.swap
cd /hive/data/genomes/ailMel1/bed/blastz.rn4.swap
time nice -n +19 doBlastzChainNet.pl -verbose=2 \
/hive/data/genomes/rn4/bed/lastzAilMel1.2010-02-04/DEF \
-swap -syntenicNet \
-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
-chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 &
# real 73m37.751s
cat fb.ailMel1.chainRn4Link.txt
# 695366144 bases of 2245312831 (30.970%) in intersection
#########################################################################
# HUMAN (hg18) PROTEINS TRACK (DONE braney 2010-04-19)
# bash if not using bash shell already
cd /cluster/data/ailMel1
mkdir /cluster/data/ailMel1/blastDb
awk '{if ($2 > 1000000) print $1}' chrom.sizes > 1meg.lst
twoBitToFa -seqList=1meg.lst ailMel1.2bit temp.fa
faSplit gap temp.fa 1000000 blastDb/x -lift=blastDb.lft
rm temp.fa 1meg.lst
awk '{if ($2 <= 1000000) print $1}' chrom.sizes > less1meg.lst
twoBitToFa -seqList=less1meg.lst ailMel1.2bit temp.fa
faSplit about temp.fa 1000000 blastDb/y
rm temp.fa less1meg.lst
cd blastDb
for i in *.fa
do
/hive/data/outside/blast229/formatdb -i $i -p F
done
rm *.fa
ls *.nsq | wc -l
# 2757
mkdir -p /cluster/data/ailMel1/bed/tblastn.hg18KG
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
echo ../../blastDb/*.nsq | xargs ls -S | sed "s/\.nsq//" > query.lst
wc -l query.lst
# 2757 query.lst
# we want around 350000 jobs
calc `wc /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl | awk '{print $1}'`/\(350000/`wc query.lst | awk '{print $1}'`\)
# 36727/(350000/2757) = 289.303826
mkdir -p kgfa
split -l 289 /cluster/data/hg18/bed/blat.hg18KG/hg18KG.psl kgfa/kg
cd kgfa
for i in *; do
nice pslxToFa $i $i.fa;
rm $i;
done
cd ..
ls -1S kgfa/*.fa > kg.lst
wc kg.lst
# 128 128 1664 kg.lst
mkdir -p blastOut
for i in `cat kg.lst`; do mkdir blastOut/`basename $i .fa`; done
tcsh
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
cat << '_EOF_' > blastGsub
#LOOP
blastSome $(path1) {check in line $(path2)} {check out exists blastOut/$(root2)/q.$(root1).psl }
#ENDLOOP
'_EOF_'
cat << '_EOF_' > blastSome
#!/bin/sh
BLASTMAT=/hive/data/outside/blast229/data
export BLASTMAT
g=`basename $2`
f=/tmp/`basename $3`.$g
for eVal in 0.01 0.001 0.0001 0.00001 0.000001 1E-09 1E-11
do
if /hive/data/outside/blast229/blastall -M BLOSUM80 -m 0 -F no -e $eVal -p tblastn -d $1 -i $2 -o $f.8
then
mv $f.8 $f.1
break;
fi
done
if test -f $f.1
then
if /cluster/bin/i386/blastToPsl $f.1 $f.2
then
liftUp -nosort -type=".psl" -nohead $f.3 /cluster/data/ailMel1/blastDb.lft carry $f.2
liftUp -nosort -type=".psl" -pslQ -nohead $3.tmp /cluster/data/hg18/bed/blat.hg18KG/protein.lft warn $f.3
if pslCheck -prot $3.tmp
then
mv $3.tmp $3
rm -f $f.1 $f.2 $f.3 $f.4
fi
exit 0
fi
fi
rm -f $f.1 $f.2 $3.tmp $f.8 $f.3 $f.4
exit 1
'_EOF_'
# << happy emacs
chmod +x blastSome
exit
ssh swarm
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
gensub2 query.lst kg.lst blastGsub blastSpec
para create blastSpec
# para try, check, push, check etc.
para time
# Completed: 352896 of 352896 jobs
# CPU time in finished jobs: 13166354s 219439.24m 3657.32h 152.39d 0.418 y
# IO & Wait Time: 1995282s 33254.69m 554.24h 23.09d 0.063 y
# Average job time: 43s 0.72m 0.01h 0.00d
# Longest finished job: 207s 3.45m 0.06h 0.00d
# Submission to last job: 15726s 262.10m 4.37h 0.18d
ssh swarm
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
mkdir chainRun
cd chainRun
tcsh
cat << '_EOF_' > chainGsub
#LOOP
chainOne $(path1)
#ENDLOOP
'_EOF_'
cat << '_EOF_' > chainOne
(cd $1; cat q.*.psl | simpleChain -prot -outPsl -maxGap=150000 stdin ../c.`basename $1`.psl)
'_EOF_'
chmod +x chainOne
ls -1dS ../blastOut/kg?? > chain.lst
gensub2 chain.lst single chainGsub chainSpec
# do the cluster run for chaining
para create chainSpec
para try, check, push, check etc.
# Completed: 128 of 128 jobs
#CPU time in finished jobs: 1401s 23.35m 0.39h 0.02d 0.000 y
#IO & Wait Time: 47407s 790.12m 13.17h 0.55d 0.002 y
#Average job time: 381s 6.36m 0.11h 0.00d
#Longest finished job: 466s 7.77m 0.13h 0.01d
#Submission to last job: 470s 7.83m 0.13h 0.01d
cd /cluster/data/ailMel1/bed/tblastn.hg18KG/blastOut
for i in kg??
do
cat c.$i.psl | awk "(\$13 - \$12)/\$11 > 0.6 {print}" > c60.$i.psl
sort -rn c60.$i.psl | pslUniq stdin u.$i.psl
awk "((\$1 / \$11) ) > 0.60 { print }" c60.$i.psl > m60.$i.psl
echo $i
done
sort u.*.psl m60* | uniq | sort -T /tmp -k 14,14 -k 16,16n -k 17,17n > ../blastHg18KG.psl
cd ..
pslCheck blastHg18KG.psl
# checked: 64037 failed: 0 errors: 0
# load table
ssh hgwdev
cd /cluster/data/ailMel1/bed/tblastn.hg18KG
hgLoadPsl ailMel1 blastHg18KG.psl
# check coverage
featureBits ailMel1 blastHg18KG
# 32308509 bases of 2245312831 (1.439%) in intersection
featureBits ailMel1 blastHg18KG xenoRefGene -enrichment
# blastHg18KG 1.439%, xenoRefGene 2.186%, both 1.137%, cover 79.05%, enrich 36.17x
rm -rf blastOut
#end tblastn