a9a2c044ff98a2ed4122c6c36dfd1a60ffcd4ba1 hiram Tue Jul 14 12:18:52 2020 -0700 working on tba experiment on chrX refs #11636 diff --git src/hg/makeDb/doc/hg38/tba10way.txt src/hg/makeDb/doc/hg38/tba10way.txt new file mode 100644 index 0000000..77d8cd1 --- /dev/null +++ src/hg/makeDb/doc/hg38/tba10way.txt @@ -0,0 +1,1915 @@ +############################################################################# +## 10-Way Multiz (DONE - 2020-07-09 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/hg38/bed/tba10way + cd /hive/data/genomes/hg38/bed/tba10way + + # from the 218-way in the source tree, select out the 10 used here: + /cluster/bin/phast/tree_doctor \ + --prune-all-but hg38,panTro5,rheMac8,mm10,canFam3,neoSch1,pteAle1,loxAfr3,monDom5,ornAna2 \ + /cluster/home/hiram/kent/src/hg/utils/phyloTrees/218way.nh \ + | sed -e 's/panTro5/panTro6/; s/rheMac8/rheMac10/; s/canFam3/canFam4/;' \ + > t.nh + + # using TreeGraph2 tree editor on the Mac, rearrange to get hg38 + # at the top, and attempt to get the others in phylo order: + /cluster/bin/phast/all_dists t.nh | grep hg38 \ + | sed -e "s/hg38.//" | sort -k2n | sed -e 's/^/#\t/;' +# panTro6 0.013390 +# rheMac10 0.079575 +# canFam4 0.332429 +# pteAle1 0.337613 +# loxAfr3 0.345811 +# neoSch1 0.374971 +# mm10 0.502391 +# monDom5 0.715679 +# ornAna2 0.953149 + + # what that looks like: +~/kent/src/hg/utils/phyloTrees/asciiTree.pl t.nh > hg38.10way.nh +~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.10way.nh | sed -e 's/^/# /;' + +# (((((((hg38:0.00655, +# panTro6:0.00684):0.029424, +# rheMac10:0.043601):0.109934, +# mm10:0.356483):0.020593, +# ((canFam4:0.054458, +# neoSch1:0.097):0.076064, +# pteAle1:0.135706):0.035406):0.023664, +# loxAfr3:0.155646):0.234728, +# monDom5:0.290786):0.071664, +# ornAna2:0.456592); + + # extract species list from that .nh file + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + hg38.10way.nh | xargs echo | sed 's/ //g; s/,/ /g' \ + | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt + + # construct db to name translation list: + cat species.list.txt | while read DB +do +hgsql -N -e "select name,organism from dbDb where name=\"${DB}\";" hgcentraltest +done | sed -e "s/\t/->/; s/ /_/g;" | sed -e 's/$/;/' | sed -e 's/\./_/g' \ + | sed -e "s#'#_x_#g;" > db.to.name.txt + +# edited db.to.name.txt to change - to _ in some of the names. +# e.g. Black_flying-fox -> Black_flying_fox, +# the flying-fox didn't survive the tree_doctor + +/cluster/bin/phast/tree_doctor --rename "`cat db.to.name.txt`" hg38.10way.nh \ + | sed -e 's/0\+)/)/g; s/0\+,/,/g' \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + | sed -e "s#_x_#'#g;" > hg38.10way.commonNames.nh + + cat hg38.10way.commonNames.nh | sed -e 's/^/# /;' +# (((((((Human:0.00655, +# Chimp:0.00684):0.029424, +# Rhesus:0.043601):0.109934, +# Mouse:0.356483):0.020593, +# ((Dog:0.054458, +# Hawaiian_monk_seal:0.097):0.076064, +# Black_flying_fox:0.135706):0.035406):0.023664, +# Elephant:0.155646):0.234728, +# Opossum:0.290786):0.071664, +# Platypus:0.456592); + +# 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_10way.png + + ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.10way.nh > t.nh + ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > hg38.10way.scientificNames.nh + rm -f t.nh + cat hg38.10way.scientificNames.nh | sed -e 's/^/# /;' +# (((((((Homo_sapiens:0.00655, +# Pan_troglodytes:0.00684):0.029424, +# Macaca_mulatta:0.043601):0.109934, +# Mus_musculus:0.356483):0.020593, +# ((Canis_lupus_familiaris:0.054458, +# Neomonachus_schauinslandi:0.097):0.076064, +# Pteropus_alecto:0.135706):0.035406):0.023664, +# Loxodonta_africana:0.155646):0.234728, +# Monodelphis_domestica:0.290786):0.071664, +# Ornithorhynchus_anatinus:0.456592); + + /cluster/bin/phast/all_dists hg38.10way.nh | grep hg38 \ + | sed -e "s/hg38.//" | sort -k2n > 10way.distances.txt + # Use this output to create the table below + cat 10way.distances.txt | sed -e 's/^/# /;' +# panTro6 0.013390 +# rheMac10 0.079575 +# canFam4 0.332429 +# pteAle1 0.337613 +# loxAfr3 0.345811 +# neoSch1 0.374971 +# mm10 0.502391 +# monDom5 0.715679 +# ornAna2 0.953149 + + printf '#!/usr/bin/env perl + +use strict; +use warnings; + +open (FH, "<10way.distances.txt") or + die "can not read 10way.distances.txt"; + +my $count = 0; +while (my $line = <FH>) { + chomp $line; + my ($D, $dist) = split('"'"'\\s+'"'"', $line); + my $chain = "chain" . ucfirst($D); + my $B="/hive/data/genomes/hg38/bed/lastz.$D/fb.hg38." . + $chain . "Link.txt"; + my $chainLinkMeasure = + `awk '"'"'{print \\$5}'"'"' ${B} 2> /dev/null | sed -e "s/(//; s/)//"`; + chomp $chainLinkMeasure; + $chainLinkMeasure = 0.0 if (length($chainLinkMeasure) < 1); + $chainLinkMeasure =~ s/\\%%//; + my $swapFile="/hive/data/genomes/${D}/bed/lastz.hg38/fb.${D}.chainHg38Link.txt"; + my $swapMeasure = "N/A"; + if ( -s $swapFile ) { + $swapMeasure = + `awk '"'"'{print \\$5}'"'"' ${swapFile} 2> /dev/null | sed -e "s/(//; s/)//"`; + chomp $swapMeasure; + $swapMeasure = 0.0 if (length($swapMeasure) < 1); + $swapMeasure =~ s/\\%%//; + } + my $orgName= + `hgsql -N -e "select organism from dbDb where name='"'"'$D'"'"';" hgcentraltest`; + chomp $orgName; + if (length($orgName) < 1) { + $orgName="N/A"; + } + ++$count; + printf "# %%02d %%.4f (%%%% %%06.3f) (%%%% %%06.3f) - %%s %%s\\n", $count, $dist, + $chainLinkMeasure, $swapMeasure, $orgName, $D; +} +close (FH); +' > sizeStats.pl + chmod +x ./sizeStats.pl + ./sizeStats.pl + +# If you can fill in all the numbers in this table, you are ready for +# the multiple alignment procedure + +# featureBits chainLink measures +# chainLink +# N distance on hg38 on other other species +# 01 0.0134 (% 95.451) (% 93.239) - Chimp panTro6 +# 02 0.0796 (% 83.855) (% 84.642) - Rhesus rheMac10 +# 03 0.3324 (% 49.808) (% 60.163) - Dog canFam4 +# 04 0.3376 (% 48.281) (% 71.168) - Black flying-fox pteAle1 +# 05 0.3458 (% 45.214) (% 42.303) - Elephant loxAfr3 +# 06 0.3750 (% 52.020) (% 61.809) - Hawaiian monk seal neoSch1 +# 07 0.5024 (% 31.653) (% 35.372) - Mouse mm10 +# 08 0.7157 (% 14.370) (% 11.996) - Opossum monDom5 +# 09 0.9531 (% 08.419) (% 12.609) - Platypus ornAna2 + +# What do all three types of chains look like: + +printf "#\t\tmafNet\tsynNet\trBest\n" + +for S in `grep -v hg38 species.list.txt` +do + rBest=`awk '{print $(NF-2)}' ../lastz.${S}/fb.*RBest* 2> /dev/null` + if [ "x${rBest}y" = "xy" ]; then + rBest="n/a" + fi + synNet=`awk '{print $(NF-2)}' ../lastz.${S}/fb.*chainSyn* 2> /dev/null` + if [ "x${synNet}y" = "xy" ]; then + synNet="n/a" + fi + mafNet=`grep intersection ../lastz.${S}/fb.* | egrep -v "RBest|chainSyn" | awk '{print $(NF-2)}'` + printf "%s\t%s\t%s\t%s\n" "${S}" "${mafNet}" "${synNet}" "${rBest}" +done + +# mafNet synNet rBest +panTro6 (95.451%) (94.807%) (89.983%) +rheMac10 (83.855%) (82.826%) (78.262%) +mm10 (31.653%) (29.964%) (29.238%) +canFam4 (49.808%) (47.849%) (45.822%) +neoSch1 (52.020%) (49.683%) (47.732%) +pteAle1 (48.281%) n/a n/a +loxAfr3 (45.214%) n/a n/a +monDom5 (14.370%) n/a n/a +ornAna2 (8.419%) n/a n/a + +# None of this concern for distances matters in building the first step, the +# maf files. The distances will be better calibrated later. + + # create species list and stripped down tree for autoMZ + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + hg38.10way.nh | xargs echo | sed 's/ //g; s/,/ /g' > tree.nh + + sed 's/[()]//g; s/,/ /g' tree.nh > species.list + cat species.list | fold -s -w 76 | sed -e 's/^/# /;' +# hg38 panTro6 rheMac10 mm10 canFam4 neoSch1 pteAle1 loxAfr3 monDom5 ornAna2 + + # bash shell syntax here ... + cd /hive/data/genomes/hg38/bed/tba10way + export H=/hive/data/genomes/hg38/bed + mkdir mafLinks + # five of them have good syntenic net: + for G in panTro6 rheMac10 mm10 canFam4 neoSch1 + 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 + + # the other four only have mafNet: + for G in pteAle1 loxAfr3 monDom5 ornAna2 + do + mkdir mafLinks/$G + echo ln -s ${H}/lastz.$G/mafNet/hg38.${G}.net.maf.gz ./mafLinks/$G + ln -s ${H}/lastz.$G/mafNet/hg38.${G}.net.maf.gz ./mafLinks/$G + done + + # verify the symLinks are good: + ls -ogL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;' +# 1105897467 Apr 3 01:43 mafLinks/canFam4/hg38.canFam4.synNet.maf.gz +# 1032494722 Apr 29 2015 mafLinks/loxAfr3/hg38.loxAfr3.net.maf.gz +# 710111073 Apr 9 2015 mafLinks/mm10/hg38.mm10.synNet.maf.gz +# 323347908 May 29 2014 mafLinks/monDom5/hg38.monDom5.net.maf.gz +# 1113427994 Mar 21 2018 mafLinks/neoSch1/hg38.neoSch1.synNet.maf.gz +# 188096324 Feb 21 2017 mafLinks/ornAna2/hg38.ornAna2.net.maf.gz +# 1669588497 Mar 25 2018 mafLinks/panTro6/hg38.panTro6.synNet.maf.gz +# 1068903277 Apr 29 2015 mafLinks/pteAle1/hg38.pteAle1.net.maf.gz +# 1386693308 Jul 3 2019 mafLinks/rheMac10/hg38.rheMac10.synNet.maf.gz + + # need to split these things up into smaller pieces for + # efficient kluster run. + mkdir /hive/data/genomes/hg38/bed/tba10way/mafSplit + cd /hive/data/genomes/hg38/bed/tba10way/mafSplit + + # mafSplitPos splits on gaps or repeat areas that will not have + # any chains, approx 5 Mbp intervals, gaps at least 10,000 + time mafSplitPos -minGap=10000 hg38 5 stdout | sort -u \ + | sort -k1,1 -k2,2n > mafSplit.bed + # real 3m3.111s + # see also multiz100way.txt for more discussion of this procedure + + # run a kluster job to split them all + # only 9 jobs, good for hgwdev cluster + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/mafSplit + + printf '#!/bin/csh -ef +set G = $1 +set M = $2 +mkdir -p $G +pushd $G > /dev/null +if ( -s hg38_${M}.00.maf ) then + /bin/rm -f hg38_${M}.*.maf +endif +/cluster/bin/x86_64/mafSplit ../mafSplit.bed hg38_ ../../mafLinks/${G}/${M}.maf.gz +/bin/gzip hg38_*.maf +popd > /dev/null +' > runOne + + # << happy emacs + chmod +x runOne + + printf '#LOOP +runOne $(dir1) $(file1) {check out exists+ $(dir1)/hg38_chr1.00.maf.gz} +#ENDLOOP +' > template + + find ../mafLinks -type l | awk -F'/' '{printf "%s/%s\n", $3,$4}' \ + | sed -e 's/.maf.gz//;' > maf.list + + gensub2 maf.list single template jobList + para -ram=16g create jobList + para try ... check ... push ... etc... +# Completed: 9 of 9 jobs +# CPU time in finished jobs: 6090s 101.51m 1.69h 0.07d 0.000 y +# IO & Wait Time: 4s 0.06m 0.00h 0.00d 0.000 y +# Average job time: 677s 11.29m 0.19h 0.01d +# Longest finished job: 1188s 19.80m 0.33h 0.01d +# Submission to last job: 1200s 20.00m 0.33h 0.01d + + # construct a list of all possible maf file names. + # they do not all exist in each of the species directories + find . -type f | grep "maf.gz" | wc -l + # 5780 + + find . -type f | grep ".maf.gz$" | xargs -L 1 basename | sort -u \ + > run.maf.list + wc -l run.maf.list + # 676 run.maf.list + + # number of chroms with data: + awk -F'.' '{print $1}' run.maf.list | sed -e 's/hg38_//;' \ + | sort | uniq -c | sort -n | wc -l + # 356 + + mkdir /hive/data/genomes/hg38/bed/tba10way/splitRun + cd /hive/data/genomes/hg38/bed/tba10way/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/tba10way/mafSplit +/bin/rm -fr $tmp +/bin/mkdir -p $tmp +/bin/cp -p ../../tree.nh ../../species.list $tmp +pushd $tmp > /dev/null +foreach s (`/bin/sed -e "s/$db //" species.list`) + set in = $pairs/$s/$c + set out = $db.$s.sing.maf + if (-e $in.gz) then + /bin/zcat $in.gz > $out + if (! -s $out) then + echo "##maf version=1 scoring=autoMZ" > $out + endif + else if (-e $in) then + /bin/ln -s $in $out + else + echo "##maf version=1 scoring=autoMZ" > $out + endif +end +set path = ($run/penn $path); rehash +$run/penn/autoMZ + T=$tmp E=$db "`cat tree.nh`" $db.*.sing.maf $c \ + > /dev/null +popd > /dev/null +/bin/rm -f $result +/bin/cp -p $tmp/$c $result +/bin/rm -fr $tmp +/bin/rmdir --ignore-fail-on-non-empty /dev/shm/$db +'_EOF_' +# << happy emacs + chmod +x autoMultiz.csh + + printf '#LOOP +./autoMultiz.csh $(root1) {check out line+ /hive/data/genomes/hg38/bed/tba10way/splitRun/maf/$(root1)} +#ENDLOOP +' > template + + ln -s ../../mafSplit/run.maf.list maf.list + + ssh ku + cd /hive/data/genomes/hg38/bed/tba10way/splitRun/run + gensub2 maf.list single template jobList + para create jobList + para try ... check ... push ... etc... +# Completed: 676 of 676 jobs +# CPU time in finished jobs: 368636s 6143.94m 102.40h 4.27d 0.012 y +# IO & Wait Time: 2457s 40.95m 0.68h 0.03d 0.000 y +# Average job time: 549s 9.15m 0.15h 0.01d +# Longest finished job: 3628s 60.47m 1.01h 0.04d +# Submission to last job: 8243s 137.38m 2.29h 0.10d + + # put the split maf results back together into a single per-chrom maf file + # eliminate duplicate comments + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/splitRun + mkdir ../maf + # no need to save the comments since they are lost with mafAddIRows + + printf '#!/bin/csh -fe +set C = $1 +if ( -s ../maf/${C}.maf.gz ) then + rm -f ../maf/${C}.maf.gz +endif +if ( -s maf/hg38_${C}.00.maf ) then + head -q -n 1 maf/hg38_${C}.00.maf | sort -u > ../maf/${C}.maf + grep -h -v "^#" `ls maf/hg38_${C}.*.maf | sort -t. -k2,2n` >> ../maf/${C}.maf + tail -q -n 1 maf/hg38_${C}.00.maf | sort -u >> ../maf/${C}.maf +else + touch ../maf/${C}.maf +endif +' > runOne + chmod +x runOne + + cat << '_EOF_' >> template + printf '#LOOP +runOne $(root1) {check out exists ../maf/$(root1).maf} +#ENDLOOP +' > template + + cut -f1 ../../../chrom.sizes > chr.list + ssh ku + cd /hive/data/genomes/hg38/bed/tba10way/splitRun + gensub2 chr.list single template jobList + para -ram=16g create jobList + para try ... check ... push ... etc ... + para -maxJob=32 push +# Completed: 640 of 640 jobs +# CPU time in finished jobs: 195s 3.25m 0.05h 0.00d 0.000 y +# IO & Wait Time: 1760s 29.33m 0.49h 0.02d 0.000 y +# Average job time: 3s 0.05m 0.00h 0.00d +# Longest finished job: 28s 0.47m 0.01h 0.00d +# Submission to last job: 157s 2.62m 0.04h 0.00d + + cd /hive/data/genomes/hg38/bed/tba10way/maf + # 284 of them have empty results, they have to be removed + ls -ogrt | awk '$3 == 0' | awk '{print $NF}' | xargs rm -f + + # Load into database + mkdir -p /gbdb/hg38/tba10way/maf + cd /hive/data/genomes/hg38/bed/tba10way/maf + ln -s `pwd`/*.maf /gbdb/hg38/tba10way/maf/ + + # this generates an immense tba10way.tab file in the directory + # where it is running. Best to run this over in scratch. + # This is going to take all day. + cd /dev/shm + time hgLoadMaf -pathPrefix=/gbdb/hg38/tba10way/maf hg38 tba10way + # Loaded 16954958 mafs in 356 files from /gbdb/hg38/tba10way/maf + # real 3m52.493s + + time (cat /gbdb/hg38/tba10way/maf/*.maf \ + | hgLoadMafSummary -verbose=2 -minSize=30000 \ + -mergeGap=1500 -maxSize=200000 hg38 tba10waySummary stdin) +# Created 1887874 summary blocks from 82903651 components and 16954958 mafs from stdin +# real 6m0.072s + +-rw-rw-r-- 1 896076678 Jul 10 09:18 tba10way.tab +-rw-rw-r-- 1 89027991 Jul 13 09:39 tba10waySummary.tab + + wc -l tba10*.tab +# 16954958 tba10way.tab +# 1887874 tba10waySummary.tab + + rm tba10way*.tab + +####################################################################### +# GAP ANNOTATE MULTIZ30WAY MAF AND LOAD TABLES (DONE - 2020-07-13 - Hiram) + # mafAddIRows has to be run on single chromosome maf files, it does not + # function correctly when more than one reference sequence + # are in a single file. + mkdir -p /hive/data/genomes/hg38/bed/tba10way/anno + cd /hive/data/genomes/hg38/bed/tba10way/anno + + # check for N.bed files everywhere: + for DB in `cat ../species.list` +do + if [ ! -s /hive/data/genomes/${DB}/${DB}.N.bed ]; then + echo "MISS: ${DB}" + cd /hive/data/genomes/${DB} + twoBitInfo -nBed ${DB}.2bit ${DB}.N.bed + else + echo " OK: ${DB}" + fi + cd /hive/data/genomes/hg38/bed/tba10way/anno +done + + cd /hive/data/genomes/hg38/bed/tba10way/anno + for DB in `cat ../species.list` +do + echo "${DB} " + ln -s /hive/data/genomes/${DB}/${DB}.N.bed ${DB}.bed + echo ${DB}.bed >> nBeds + ln -s /hive/data/genomes/${DB}/chrom.sizes ${DB}.len + echo ${DB}.len >> sizes +done + # make sure they all are successful symLinks: + ls -ogrtL *.bed | wc -l + # 30 + + screen -S hg38 # use a screen to control this longish job + ssh ku + cd /hive/data/genomes/hg38/bed/tba10way/anno + mkdir result + + printf '#LOOP +mafAddIRows -nBeds=nBeds $(path1) /hive/data/genomes/hg38/hg38.2bit {check out line+ result/$(file1)} +#ENDLOOP +' > template + # << happy emacs + + ls ../maf/*.maf > maf.list + gensub2 maf.list single template jobList + # no need to limit these jobs, there are only 358 of them + para -ram=64g create jobList + para try ... check ... + para -maxJob=10 push +# Completed: 356 of 356 jobs +# CPU time in finished jobs: 669s 11.15m 0.19h 0.01d 0.000 y +# IO & Wait Time: 1015s 16.92m 0.28h 0.01d 0.000 y +# Average job time: 5s 0.08m 0.00h 0.00d +# Longest finished job: 56s 0.93m 0.02h 0.00d +# Submission to last job: 152s 2.53m 0.04h 0.00d + + du -hsc result + # 30G result + + # Load into database + rm -f /gbdb/hg38/tba10way/maf/* + cd /hive/data/genomes/hg38/bed/tba10way/anno/result + + ln -s `pwd`/*.maf /gbdb/hg38/tba10way/maf/ + + # this generates an immense tba10way.tab file in the directory + # where it is running. Best to run this over in scratch. + cd /dev/shm + time hgLoadMaf -pathPrefix=/gbdb/hg38/tba10way/maf hg38 multiz10way + # Loaded 17000572 mafs in 356 files from /gbdb/hg38/tba10way/maf + # real 5m10.599s + + + # -rw-rw-r-- 1 900843709 Jul 13 11:01 multiz10way.tab + + time (cat /gbdb/hg38/tba10way/maf/*.maf \ + | hgLoadMafSummary -verbose=2 -minSize=30000 \ + -mergeGap=1500 -maxSize=200000 hg38 multiz10waySummary stdin) +# Created 1887874 summary blocks from 82903651 components and 17000572 mafs from stdin +# real 7m15.373s + +# -rw-rw-r-- 1 900843709 Jul 13 11:01 multiz10way.tab +# -rw-rw-r-- 1 92803739 Jul 13 11:10 multiz10waySummary.tab + + wc -l multiz10way*.tab + # 17000572 multiz10way.tab + # 1887874 multiz10waySummary.tab + + rm multiz10way*.tab + +############################################################################## +# MULTIZ7WAY MAF FRAMES (DONE - 2020-07-13 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/hg38/bed/tba10way/frames + cd /hive/data/genomes/hg38/bed/tba10way/frames +# survey all the genomes to find out what kinds of gene tracks they have + + printf '#!/bin/csh -fe +foreach db (`cat ../species.list`) + echo -n "# ${db}: " + set tables = `hgsql $db -N -e "show tables" | egrep "Gene|ncbiRefSeq"` + foreach table ($tables) + if ($table == "ensGene" || $table == "refGene" || \ + $table == "ncbiRefSeq" || $table == "ncbiRefSeqCurated" || \ + $table == "ncbiRefSeqPredicted" || $table == "mgcGenes" || \ + $table == "knownGene" || $table == "xenoRefGene" ) then + set count = `hgsql $db -N -e "select count(*) from $table"` + echo -n "${table}: ${count}, " + endif + end + echo +end +' > showGenes.csh + + chmod +x ./showGenes.csh + time ./showGenes.csh +# hg38: ensGene: 208239, knownGene: 247541, mgcGenes: 36638, ncbiRefSeq: 166923, ncbiRefSeqCurated: 78591, ncbiRefSeqPredicted: 88332, refGene: 86303, xenoRefGene: 199483, +# panTro6: ncbiRefSeq: 102471, ncbiRefSeqCurated: 2711, ncbiRefSeqPredicted: 99760, refGene: 2873, xenoRefGene: 242030, +# rheMac10: ensGene: 64191, ncbiRefSeq: 86732, ncbiRefSeqCurated: 6375, ncbiRefSeqPredicted: 80357, refGene: 6481, xenoRefGene: 240078, +# mm10: ensGene: 103734, knownGene: 142446, mgcGenes: 27606, ncbiRefSeq: 106520, ncbiRefSeqCurated: 34892, ncbiRefSeqPredicted: 71628, refGene: 46131, xenoRefGene: 190941, +# canFam4: refGene: 2380, xenoRefGene: 235387, +# neoSch1: ncbiRefSeq: 29897, ncbiRefSeqCurated: 13, ncbiRefSeqPredicted: 29884, xenoRefGene: 440659, +# pteAle1: ncbiRefSeq: 46978, ncbiRefSeqCurated: 32, ncbiRefSeqPredicted: 46946, +# loxAfr3: ensGene: 28847, ncbiRefSeq: 46056, ncbiRefSeqCurated: 35, ncbiRefSeqPredicted: 46021, refGene: 23, xenoRefGene: 355734, +# monDom5: ensGene: 32358, refGene: 1238, xenoRefGene: 254747, +# ornAna2: ensGene: 31006, refGene: 705, xenoRefGene: 699826, + +# real 0m1.884s + + # from that summary, use these gene sets: + # ncbiRefSeqCurated - hg38 mm10 + # ncbiRefSeq - panTro6 rheMac10 neoSch1 pteAle1 loxAfr3 + # ensGene - monDom5 ornAna2 + # xenoRefGene - canFam4 + + mkdir genes + + # 1. ncbiRefSeqCurated: hg38 mm10 + for DB in hg38 mm10 +do + hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from ncbiRefSeqCurated" ${DB} \ + | genePredSingleCover stdin stdout | gzip -2c \ + > genes/${DB}.gp.gz + echo -n "# ${DB}: " + genePredCheck -db=${DB} genes/${DB}.gp.gz 2>&1 | sed -e 's/^/ # /;' +done +# hg38: # checked: 21740 failed: 0 +# mm10: # checked: 20520 failed: 0 + + # 2. ncbiRefSeq: panTro6 rheMac10 neoSch1 pteAle1 loxAfr3 + for DB in panTro6 rheMac10 neoSch1 pteAle1 loxAfr3 +do +hgsql -N -e "select +name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds +from ncbiRefSeq" ${DB} \ + | genePredSingleCover stdin stdout | gzip -2c \ + > /dev/shm/${DB}.tmp.gz + mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz + echo -n "# ${DB}: " + genePredCheck -db=${DB} genes/${DB}.gp.gz +done +# panTro6: checked: 21380 failed: 0 +# rheMac10: checked: 21021 failed: 0 +# neoSch1: checked: 18783 failed: 0 +# pteAle1: checked: 18326 failed: 0 +# loxAfr3: checked: 21061 failed: 0 + + # 3. ensGene: monDom5 ornAna2 + for DB in monDom5 ornAna2 +do + hgsql -N -e "select +name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds +from ensGene" ${DB} \ + | genePredSingleCover stdin stdout | gzip -2c \ + > /dev/shm/${DB}.tmp.gz + mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz + echo -n "# ${DB}: " + genePredCheck -db=${DB} genes/${DB}.gp.gz +done +# monDom5: checked: 21033 failed: 0 +# ornAna2: checked: 21311 failed: 0 + + # 4. refGene: canFam4 + for DB in canFam4 +do + hgsql -N -e "select +name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds +from xenoRefGene" ${DB} \ + | genePredSingleCover stdin stdout | gzip -2c \ + > /dev/shm/${DB}.tmp.gz + mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz + echo -n "# ${DB}: " + genePredCheck -db=${DB} genes/${DB}.gp.gz +done +# canFam4: checked: 20110 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/canFam4.gp.gz: 19188 +# genes/hg38.gp.gz: 19211 +# genes/loxAfr3.gp.gz: 21061 +# genes/mm10.gp.gz: 20520 +# genes/monDom5.gp.gz: 21033 +# genes/neoSch1.gp.gz: 18783 +# genes/ornAna2.gp.gz: 21311 +# genes/panTro6.gp.gz: 21376 +# genes/pteAle1.gp.gz: 18326 +# genes/rheMac10.gp.gz: 21020 + + # kluster job to annotate each maf file + screen -S hg38 # manage long running procedure with screen + ssh ku + cd /hive/data/genomes/hg38/bed/tba10way/frames + + printf '#!/bin/csh -fe + +set C = $1 +set G = $2 + +cat ../maf/${C}.maf | genePredToMafFrames hg38 stdin stdout \ + ${G} genes/${G}.gp.gz | gzip > parts/${C}.${G}.mafFrames.gz +' > runOne + + chmod +x runOne + + ls ../maf | sed -e "s/.maf//" > chr.list + ls genes | sed -e "s/.gp.gz//" > gene.list + + printf '#LOOP +runOne $(root1) $(root2) {check out exists+ parts/$(root1).$(root2).mafFrames.gz} +#ENDLOOP +' > template + + mkdir parts + gensub2 chr.list gene.list template jobList + para -ram=64g create jobList + para try ... check ... push +# Completed: 3560 of 3560 jobs +# CPU time in finished jobs: 3386s 56.43m 0.94h 0.04d 0.000 y +# IO & Wait Time: 8419s 140.32m 2.34h 0.10d 0.000 y +# Average job time: 3s 0.06m 0.00h 0.00d +# Longest finished job: 19s 0.32m 0.01h 0.00d +# Submission to last job: 753s 12.55m 0.21h 0.01d + + # collect all results into one file: + cd /hive/data/genomes/hg38/bed/tba10way/frames + time find ./parts -type f | while read F +do + echo "${F}" 1>&2 + zcat ${F} +done | sort -k1,1 -k2,2n > multiz10wayFrames.bed + # real 0m44.679s + + # -rw-rw-r-- 1 227919888 Jul 13 10:52 multiz10wayFrames.bed + + gzip multiz10wayFrames.bed + + # verify there are frames on everything, should be 46 species: + # (count from: ls genes | wc) + zcat multiz10wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \ + | sed -e 's/^/# /;' > species.check.list + wc -l species.check.list + # 10 + +# 243766 canFam4 +# 210024 hg38 +# 389932 loxAfr3 +# 251743 mm10 +# 570387 monDom5 +# 252141 neoSch1 +# 589907 ornAna2 +# 225700 panTro6 +# 380179 pteAle1 +# 236549 rheMac10 + + # load the resulting file + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/frames + time hgLoadMafFrames hg38 multiz10wayFrames multiz10wayFrames.bed.gz + # real 0m21.014s + + hgsql -e 'select count(*) from multiz10wayFrames;' hg38 + # +----------+ + # | count(*) | + # +----------+ + # | 3350328 | + # +----------+ + + time featureBits -countGaps hg38 multiz10wayFrames + # 64900367 bases of 3272116950 (1.983%) in intersection + # real 0m18.824s + + # enable the trackDb entries: +# frames multiz10wayFrames +# irows on + # zoom to base level in an exon to see codon displays + # appears to work OK + +######################################################################### +## Experiment running tba on just chrX alignments (DONE - 2020-07-14 - Hiram) + + mkdir /hive/data/genomes/hg38/bed/tba10way/chrX + cd /hive/data/genomes/hg38/bed/tba10way/chrX + mkdir fasta + # six of these species have chrX which corresponds to hg38 chrX + # so use that sequence directly, the fasta header line is formatted + # to correspond with desired meta info to be used by tba/multiz tools: + for S in hg38 panTro6 rheMac10 mm10 canFam4 monDom5 +do + size=`grep -w chrX /hive/data/genomes/${S}/chrom.sizes | awk '{print $2}'` + twoBitToFa /hive/data/genomes/$S/$S.2bit:chrX stdout \ + | sed -e "s#>.*#>$S:chrX:1:+:$size##;" > fasta/$S.fa +done + +######################################################################### +# Phylogenetic tree from 30-way (DONE - 2013-09-13 - Hiram) + mkdir /hive/data/genomes/hg38/bed/tba10way/4d + cd /hive/data/genomes/hg38/bed/tba10way/4d + + # the annotated maf's are in: + ../anno/result/*.maf + + # using knownGene for hg38, only transcribed genes and nothing + # from the randoms and other misc. + hgsql -Ne "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene where cdsEnd > cdsStart;" hg38 \ + | egrep -E -v "chrM|chrUn|random|_alt" > knownGene.gp + wc -l *.gp + # 95199 knownGene.gp + + # verify it is only on the chroms: + cut -f2 knownGene.gp | sort | uniq -c | sort -rn | sed -e 's/^/ # /;' + # 7956 chr1 + # 7306 chr19 + # 6554 chr17 + # 6371 chr11 + # 6301 chr2 + # 5794 chr12 + # 5688 chr3 + # 4971 chr16 + # 4324 chr7 + # 4277 chr6 + # 4108 chr5 + # 3751 chr14 + # 3622 chr4 + # 3580 chr8 + # 3364 chr15 + # 3076 chrX + # 2968 chr10 + # 2961 chr9 + # 2107 chr22 + # 2091 chr20 + # 1703 chr18 + # 1175 chr13 + # 935 chr21 + # 216 chrY + + genePredSingleCover knownGene.gp stdout | sort > knownGeneNR.gp + wc -l knownGeneNR.gp + # 19306 knownGeneNR.gp + + ssh ku + mkdir /hive/data/genomes/hg38/bed/tba10way/4d/run + cd /hive/data/genomes/hg38/bed/tba10way/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/tba10way" +set c = $1 +set infile = $r/anno/result/$2 +set outfile = $3 +cd /dev/shm +# 'clean' maf, removes all chrom names, leaves only the db name +perl -wpe 's/^s ([^.]+)\.\S+/s $1/' $infile > $c.maf +awk -v C=$c '$2 == C {print}' $r/4d/knownGeneNR.gp | sed -e "s/\t$c\t/\thg38.$c\t/" > $c.gp +set NL=`wc -l $c.gp| gawk '{print $1}'` +if ("$NL" != "0") then + $PHASTBIN/msa_view --4d --features $c.gp -i MAF $c.maf -o SS > $c.ss + $PHASTBIN/msa_view -i SS --tuple-size 1 $c.ss > $r/4d/run/$outfile +else + echo "" > $r/4d/run/$outfile +endif +rm -f $c.gp $c.maf $c.ss +'_EOF_' + # << happy emacs + chmod +x 4d.csh + + ls -1S /hive/data/genomes/hg38/bed/tba10way/anno/result/*.maf \ + | sed -e "s#.*tba10way/anno/result/##" \ + | egrep -E -v "chrM|chrUn|random|_alt" > maf.list + + printf '#LOOP +4d.csh $(root1) $(path1) {check out line+ ../mfa/$(root1).mfa} +#ENDLOOP +' > template + + gensub2 maf.list single template jobList + para -ram=64g create jobList + para try ... check ... push ... etc... + para time +# Completed: 24 of 24 jobs +# CPU time in finished jobs: 7202s 120.03m 2.00h 0.08d 0.000 y +# IO & Wait Time: 480s 8.00m 0.13h 0.01d 0.000 y +# Average job time: 320s 5.33m 0.09h 0.00d +# Longest finished job: 706s 11.77m 0.20h 0.01d +# Submission to last job: 718s 11.97m 0.20h 0.01d + + # combine mfa files + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/4d + # verify no tiny files: + ls -og mfa | sort -k3nr | tail -2 + # -rw-rw-r-- 1 235884 Nov 3 11:25 chrY.mfa + + #want comma-less species.list + time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_view \ + --aggregate "`cat ../species.list`" mfa/*.mfa | sed s/"> "/">"/ \ + > 4d.all.mfa + # real 0m3.182s + + # check they are all in there: + grep "^>" 4d.all.mfa | wc -l + # 30 + + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + hg38.10way.nh + + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + ../hg38.10way.nh > tree-commas.nh + + # use phyloFit to create tree model (output is phyloFit.mod) + time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/phyloFit \ + --EM --precision MED --msa-format FASTA --subst-mod REV \ + --tree tree-commas.nh 4d.all.mfa + # real 8m6.444s + + mv phyloFit.mod all.mod + + grep TREE all.mod +# ((((((((((((hg38:0.0101811,panTro5:0.00256557):0.00168527, +# panPan2:0.00255779):0.00567544,gorGor5:0.00857055):0.0093291, +# ponAbe2:0.0183757):0.00328934,nomLeu3:0.022488):0.0111201, +# (((((rheMac8:0.00266214,(macFas5:0.00218171, +# macNem1:0.00424092):0.00171674):0.00606702,cerAty1:0.00671556):0.00164923, +# papAnu3:0.00691761):0.00171877,(chlSab2:0.0163497, +# manLeu1:0.00699129):0.00165863):0.00933639,((nasLar1:0.00768293, +# colAng1:0.0163932):0.00167418,(rhiRox1:0.00213201, +# rhiBie1:0.00222829):0.00577271):0.0104228):0.0214064):0.0206136, +# (((calJac3:0.0358464,saiBol1:0.0324064):0.00173657, +# cebCap1:0.0283117):0.00202114,aotNan1:0.0232387):0.0378592):0.0606754, +# tarSyr2:0.142222):0.011174,(((micMur3:0.0563648, +# proCoq1:0.0388184):0.00530425,(eulMac1:0.00218443, +# eulFla1:0.00228562):0.0410542):0.0370791, +# otoGar3:0.132725):0.0335535):0.0178619,mm10:0.344583):0.0241482, +# canFam3:0.163902):0.0880829,dasNov3:0.0880829); + + # compare these calculated lengths to what we started with + + /cluster/bin/phast/all_dists ../hg38.10way.nh | grep hg38 \ + | sed -e "s/hg38.//;" | sort > original.dists + + grep TREE all.mod | sed -e 's/TREE: //;' \ + | /cluster/bin/phast/all_dists /dev/stdin | grep hg38 \ + | sed -e "s/hg38.//;" | sort > hg38.dists + + # printing out the 'original', the 'new' the 'difference' and + # percent difference/delta + join original.dists hg38.dists | awk '{ + printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%8.6f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }' | sort -k4n +# panTro5 0.013390 0.012747 0.000643 5.044324 +# panPan2 0.015610 0.014424 0.001186 8.222407 +# gorGor5 0.019734 0.026112 -0.006378 -24.425551 +# ponAbe2 0.039403 0.045247 -0.005844 -12.915773 +# nomLeu3 0.046204 0.052648 -0.006444 -12.239781 +# papAnu3 0.079626 0.080660 -0.001034 -1.281924 +# manLeu1 0.090974 0.080673 0.010301 12.768832 +# rhiRox1 0.075474 0.081014 -0.005540 -6.838324 +# rhiBie1 0.075474 0.081111 -0.005637 -6.949736 +# cerAty1 0.082584 0.082107 0.000477 0.580949 +# nasLar1 0.075474 0.082467 -0.006993 -8.479756 +# rheMac8 0.079575 0.084120 -0.004545 -5.402996 +# macFas5 0.079575 0.085357 -0.005782 -6.773903 +# macNem1 0.081584 0.087416 -0.005832 -6.671548 +# chlSab2 0.087974 0.090031 -0.002057 -2.284769 +# colAng1 0.075574 0.091177 -0.015603 -17.112868 +# aotNan1 0.102804 0.122992 -0.020188 -16.414076 +# cebCap1 0.108804 0.130086 -0.021282 -16.359946 +# saiBol1 0.087804 0.135917 -0.048113 -35.398810 +# calJac3 0.107454 0.139357 -0.031903 -22.893001 +# eulMac1 0.190934 0.247615 -0.056681 -22.890778 +# eulFla1 0.190934 0.247716 -0.056782 -22.922217 +# proCoq1 0.230934 0.248499 -0.017565 -7.068439 +# tarSyr2 0.221294 0.264791 -0.043497 -16.426918 +# micMur3 0.236534 0.266045 -0.029511 -11.092484 +# otoGar3 0.270334 0.300022 -0.029688 -9.895274 +# canFam3 0.332429 0.339655 -0.007226 -2.127453 +# dasNov3 0.366691 0.351919 0.014772 4.197557 +# mm10 0.502391 0.496188 0.006203 1.250131 + +######################################################################### +# phastCons 30-way (DONE - 2015-05-07 - Hiram) + # split 10way mafs into 10M chunks and generate sufficient statistics + # files for # phastCons + ssh ku + mkdir -p /hive/data/genomes/hg38/bed/tba10way/cons/ss + mkdir -p /hive/data/genomes/hg38/bed/tba10way/cons/msa.split + cd /hive/data/genomes/hg38/bed/tba10way/cons/msa.split + + cat << '_EOF_' > doSplit.csh +#!/bin/csh -ef +set c = $1 +set MAF = /hive/data/genomes/hg38/bed/tba10way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/hg38/bed/tba10way/cons/ss/$c +set WC = `cat $MAF | wc -l` +set NL = `grep "^#" $MAF | wc -l` +if ( -s $2 ) then + exit 0 +endif +if ( -s $2.running ) then + exit 0 +endif + +date >> $2.running + +rm -fr $WINDOWS +mkdir $WINDOWS +pushd $WINDOWS > /dev/null +if ( $WC != $NL ) then +/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \ + $MAF -i MAF -o SS -r $WINDOWS/$c -w 3000000,0 -I 300 -B 5000 +endif +popd > /dev/null +date >> $2 +rm -f $2.running +'_EOF_' + # << happy emacs + chmod +x doSplit.csh + + cat << '_EOF_' > template + printf '#LOOP +doSplit.csh $(root1) {check out line+ $(root1).done} +#ENDLOOP +' > template + +F_' > doSplit.csh +#!/bin/csh -ef +set c = $1 +set MAF = /hive/data/genomes/hg38/bed/tba10way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/hg38/bed/tba10way/cons/ss/$c +set WC = `cat $MAF | wc -l` +set NL = `grep "^#" $MAF | wc -l` +if ( -s $2 ) then + exit 0 +endif +if ( -s $2.running ) then + exit 0 +endif + +date >> $2.running + +rm -fr $WINDOWS +mkdir $WINDOWS +pushd $WINDOWS > /dev/null +if ( $WC != $NL ) then +/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \ + $MAF -i MAF -o SS -r $WINDOWS/$c -w 3000000,0 -I 300 -B 5000 +endif +popd > /dev/null +date >> $2 +rm -f $2.running +'_EOF_' + # << happy emacs + chmod +x doSplit.csh + + cat << '_EOF_' > template +#LOOP +doSplit.csh $(root1) {check out line+ $(root1).done} +#ENDLOOP + +# do the easy ones first to see some immediate results + ls -1S -r ../../anno/result | sed -e "s/.maf//;" > maf.list + # all can finish OK at a 64Gb memory limit + gensub2 maf.list single template jobList + para -ram=64g create jobList + para try ... check ... etc + para push +# Completed: 358 of 358 jobs +# CPU time in finished jobs: 13099s 218.32m 3.64h 0.15d 0.000 y +# IO & Wait Time: 1841s 30.68m 0.51h 0.02d 0.000 y +# Average job time: 42s 0.70m 0.01h 0.00d +# Longest finished job: 1393s 23.22m 0.39h 0.02d +# Submission to last job: 1468s 24.47m 0.41h 0.02d + + # Run phastCons + # This job is I/O intensive in its output files, beware where this + # takes place or do not run too many at once. + ssh ku + mkdir -p /hive/data/genomes/hg38/bed/tba10way/cons/run.cons + cd /hive/data/genomes/hg38/bed/tba10way/cons/run.cons + + # This is setup for multiple runs based on subsets, but only running + # the 'all' subset here. + # It triggers off of the current working directory + # $cwd:t which is the "grp" in this script. Running: + # all and vertebrates + + cat << '_EOF_' > doPhast.csh +#!/bin/csh -fe +set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin +set c = $1 +set f = $2 +set len = $3 +set cov = $4 +set rho = $5 +set grp = $cwd:t +set cons = /hive/data/genomes/hg38/bed/tba10way/cons +set tmp = $cons/tmp/$f +mkdir -p $tmp +set ssSrc = $cons/ss +set useGrp = "$grp.mod" +if (-s $cons/$grp/$grp.non-inf) then + ln -s $cons/$grp/$grp.mod $tmp + ln -s $cons/$grp/$grp.non-inf $tmp + ln -s $ssSrc/$c/$f.ss $tmp +else + ln -s $ssSrc/$c/$f.ss $tmp + ln -s $cons/$grp/$grp.mod $tmp +endif +pushd $tmp > /dev/null +if (-s $grp.non-inf) then + $PHASTBIN/phastCons $f.ss $useGrp \ + --rho $rho --expected-length $len --target-coverage $cov --quiet \ + --not-informative `cat $grp.non-inf` \ + --seqname $c --idpref $c --most-conserved $f.bed --score > $f.pp +else + $PHASTBIN/phastCons $f.ss $useGrp \ + --rho $rho --expected-length $len --target-coverage $cov --quiet \ + --seqname $c --idpref $c --most-conserved $f.bed --score > $f.pp +endif +popd > /dev/null +mkdir -p pp/$c bed/$c +sleep 4 +touch pp/$c bed/$c +rm -f pp/$c/$f.pp +rm -f bed/$c/$f.bed +mv $tmp/$f.pp pp/$c +mv $tmp/$f.bed bed/$c +rm -fr $tmp +'_EOF_' + # << happy emacs + chmod +x doPhast.csh + + # this template will serve for all runs + # root1 == chrom name, file1 == ss file name without .ss suffix + printf '#LOOP +../run.cons/doPhast.csh $(root1) $(file1) 45 0.3 0.3 {check out line+ pp/$(root1)/$(file1).pp} +#ENDLOOP +' > template + + ls -1S ../ss/chr*/chr* | sed -e "s/.ss$//" > ss.list + wc -l ss.list + # 1337 ss.list + + # Create parasol batch and run it + # run for all species + cd /hive/data/genomes/hg38/bed/tba10way/cons + mkdir -p all + cd all + # Using the .mod tree + cp -p ../../4d/all.mod ./all.mod + + gensub2 ../run.cons/ss.list single ../run.cons/template jobList + # beware overwhelming the cluster with these fast running high I/O jobs + para -ram=32g create jobList + para try ... check ... + para -maxJob=16 push +# Completed: 1337 of 1337 jobs +# CPU time in finished jobs: 17323s 288.72m 4.81h 0.20d 0.001 y +# IO & Wait Time: 9727s 162.11m 2.70h 0.11d 0.000 y +# Average job time: 20s 0.34m 0.01h 0.00d +# Longest finished job: 31s 0.52m 0.01h 0.00d +# Submission to last job: 230s 3.83m 0.06h 0.00d + + # create Most Conserved track + cd /hive/data/genomes/hg38/bed/tba10way/cons/all + time cut -f1 ../../../../chrom.sizes | while read C +do + echo $C 1>&2 + ls -d bed/${C} 2> /dev/null | while read D + do + cat ${D}/${C}*.bed + done | sort -k1,1 -k2,2n \ + | awk '{printf "%s\t%d\t%d\tlod=%d\t%s\n", "'${C}'", $2, $3, $5, $5;}' +done > tmpMostConserved.bed + # real 0m50.678s + + # -rw-rw-r-- 1 101245734 Nov 3 14:20 tmpMostConserved.bed + + time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \ + > mostConserved.bed + # real 0m24.196s + + # -rw-rw-r-- 1 103966297 Nov 3 14:21 mostConserved.bed + + # load into database + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/cons/all + time hgLoadBed hg38 phastConsElements10way mostConserved.bed + # Read 2949865 elements of size 5 from mostConserved.bed + # real 0m26.263s + + # --rho 0.3 --expected-length 45 --target-coverage 0.3 + time featureBits hg38 -enrichment knownGene:cds phastConsElements10way +# knownGene:cds 1.271%, phastConsElements10way 5.795%, both 0.874%, cover 68.73%, enrich 11.86x +# real 0m21.637s + + # Try for 5% overall cov, and 70% CDS cov + time featureBits hg38 -enrichment refGene:cds phastConsElements10way +# refGene:cds 1.225%, phastConsElements10way 5.795%, both 0.863%, cover 70.50%, enrich 12.16x + +# real 0m22.260s + + # Create merged posterier probability file and wiggle track data files + cd /hive/data/genomes/hg38/bed/tba10way/cons/all + mkdir downloads + + time for D in `ls -d pp/chr* | sed -e 's#pp/##'` +do + echo "working: $D" 1>&2 + find ./pp/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ + | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ + | gzip -c > downloads/${D}.phastCons10way.wigFix.gz +done + # real 32m29.089s + + + # encode those files into wiggle data + time (zcat downloads/*.wigFix.gz \ + | wigEncode stdin phastCons10way.wig phastCons10way.wib) + # Converted stdin, upper limit 1.00, lower limit 0.00 + # real 15m40.010s + + du -hsc *.wi? + # 2.8G phastCons10way.wib + # 283M phastCons10way.wig + + # encode into a bigWig file: + # (warning wigToBigWig process may be too large for memory limits + # in bash, to avoid the 32 Gb memory limit, set 180 Gb here: +export sizeG=188743680 +ulimit -d $sizeG +ulimit -v $sizeG + time (zcat downloads/*.wigFix.gz \ + | wigToBigWig -verbose=2 stdin \ + ../../../../chrom.sizes phastCons10way.bw) > bigWig.log 2>&1 + egrep "VmPeak|real" bigWig.log + # pid=37111: VmPeak: 33886864 kB + # real 42m13.614s + + # -rw-rw-r-- 1 7077152013 Nov 6 08:52 phastCons10way.bw + + + bigWigInfo phastCons10way.bw +version: 4 +isCompressed: yes +isSwapped: 0 +primaryDataSize: 5,097,637,987 +primaryIndexSize: 93,372,648 +zoomLevels: 10 +chromCount: 355 +basesCovered: 2,955,660,600 +mean: 0.128025 +min: 0.000000 +max: 1.000000 +std: 0.247422 + + # if you wanted to use the bigWig file, loading bigWig table: + # but we don't use the bigWig file + mkdir /gbdb/hg38/bbi + ln -s `pwd`/phastCons10way.bw /gbdb/hg38/bbi + hgsql hg38 -e 'drop table if exists phastCons10way; \ + create table phastCons10way (fileName varchar(255) not null); \ + insert into phastCons10way values + ("/gbdb/hg38/bbi/phastCons10way.bw");' + + # Load gbdb and database with wiggle. + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/cons/all + ln -s `pwd`/phastCons10way.wib /gbdb/hg38/tba10way/phastCons10way.wib + time hgLoadWiggle -pathPrefix=/gbdb/hg38/tba10way hg38 \ + phastCons10way phastCons10way.wig + # real 0m32.272s + + time wigTableStats.sh hg38 phastCons10way +# db.table min max mean count sumData +# hg38.phastCons10way 0 1 0.128025 2955660600 3.78397e+08 +# stdDev viewLimits +# 0.247422 viewLimits=0:1 +# real 0m13.507s + + # Create histogram to get an overview of all the data + ssh hgwdev + cd /hive/data/genomes/hg38/bed/tba10way/cons/all + time hgWiggle -doHistogram -db=hg38 \ + -hBinSize=0.001 -hBinCount=300 -hMinVal=0.0 -verbose=2 \ + phastCons10way > histogram.data 2>&1 + # real 2m38.952s + + # create plot of histogram: + + printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \ +"/usr/share/fonts/default/Type1/n022004l.pfb" +set size 1.4, 0.8 +set key left box +set grid noxtics +set grid ytics +set title " Human Hg38 Histogram phastCons10way track" +set xlabel " phastCons10way score" +set ylabel " Relative Frequency" +set y2label " Cumulative Relative Frequency (CRF)" +set y2range [0:1] +set y2tics +set yrange [0:0.02] + +plot "histogram.data" using 2:5 title " RelFreq" with impulses, \ + "histogram.data" using 2:7 axes x1y2 title " CRF" with lines +' | gnuplot > histo.png + + # take a look to see if it is sane: + + display histo.png & + +######################################################################### +# phyloP for 30-way (DONE - 2017-11-06 - Hiram) +# + # split SS files into 1M chunks, this business needs smaller files + # to complete + + ssh ku + mkdir /hive/data/genomes/hg38/bed/tba10way/consPhyloP + cd /hive/data/genomes/hg38/bed/tba10way/consPhyloP + mkdir ss run.split + cd run.split + + printf '#!/bin/csh -ef +set c = $1 +set MAF = /hive/data/genomes/hg38/bed/tba10way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/hg38/bed/tba10way/consPhyloP/ss/$c +set WC = `cat $MAF | wc -l` +set NL = `grep "^#" $MAF | wc -l` +if ( -s $2 ) then + exit 0 +endif +if ( -s $2.running ) then + exit 0 +endif + +date >> $2.running + +rm -fr $WINDOWS +mkdir -p $WINDOWS +pushd $WINDOWS > /dev/null +if ( $WC != $NL ) then +/cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_split \ + $MAF -i MAF -o SS -r $WINDOWS/$c -w 1000000,0 -I 1000 -B 5000 +endif +popd > /dev/null +date >> $2 +rm -f $2.running +' > doSplit.csh + + chmod +x doSplit.csh + + # do the easy ones first to see some immediate results + ls -1S -r ../../anno/result | sed -e "s/.maf//;" > maf.list + + # this needs a {check out line+ $(root1.done)} test for verification: + printf '#LOOP +./doSplit.csh $(root1) $(root1).done +#ENDLOOP +' > template + + gensub2 maf.list single template jobList + # all can complete successfully at the 64Gb memory limit + para -ram=64g create jobList + para try ... check ... push ... etc... + +# Completed: 358 of 358 jobs +# CPU time in finished jobs: 13512s 225.20m 3.75h 0.16d 0.000 y +# IO & Wait Time: 1646s 27.43m 0.46h 0.02d 0.000 y +# Average job time: 42s 0.71m 0.01h 0.00d +# Longest finished job: 1494s 24.90m 0.41h 0.02d +# Submission to last job: 1717s 28.62m 0.48h 0.02d + + # run phyloP with score=LRT + ssh ku + mkdir /cluster/data/hg38/bed/tba10way/consPhyloP + cd /cluster/data/hg38/bed/tba10way/consPhyloP + + mkdir run.phyloP + cd run.phyloP + # Adjust model file base composition background and rate matrix to be + # representative of the chromosomes in play + grep BACK ../../4d/all.mod + # BACKGROUND: 0.207173 0.328301 0.237184 0.227343 + + grep BACKGROUND ../../4d/all.mod | awk '{printf "%0.3f\n", $3 + $4}' + # 0.565 + /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \ + ../../4d/all.mod 0.565 > all.mod + # verify, the BACKGROUND should now be paired up: + grep BACK all.mod + # BACKGROUND: 0.217500 0.282500 0.282500 0.217500 + + printf '#!/bin/csh -fe +set PHASTBIN = /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin +set f = $1 +set ssFile = $1:t +set out = $2 +set cName = $f:h +set n = $f:r:e +set grp = $cwd:t +set cons = /hive/data/genomes/hg38/bed/tba10way/consPhyloP +set tmp = $cons/tmp/$grp/$f +/bin/rm -fr $tmp +/bin/mkdir -p $tmp +set ssSrc = "$cons/ss/$cName/$ssFile" +set useGrp = "$grp.mod" +/bin/ln -s $cons/run.phyloP/$grp.mod $tmp +pushd $tmp > /dev/null +echo source: $ssSrc.ss +$PHASTBIN/phyloP --method LRT --mode CONACC --wig-scores --chrom $cName \ + -i SS $useGrp $ssSrc.ss > $ssFile.wigFix +popd > /dev/null +/bin/mkdir -p $out:h +sleep 4 +/bin/touch $out:h +/bin/mv $tmp/$ssFile.wigFix $out +/bin/rm -fr $tmp +/bin/rmdir --ignore-fail-on-non-empty $cons/tmp/$grp +/bin/rmdir --ignore-fail-on-non-empty $cons/tmp +' > doPhyloP.csh + + chmod +x doPhyloP.csh + + # Create list of chunks + find ../ss -type f | sed -e "s/.ss$//; s#../ss/##;" > ss.list + # make sure the list looks good + wc -l ss.list + # 3308 ss.list + + # Create template file + # file1 == $chr/$chunk/file name without .ss suffix + printf '#LOOP +../run.phyloP/doPhyloP.csh $(path1) {check out line+ wigFix/$(dir1)/$(file1).wigFix} +#ENDLOOP +' > template + + ###################### Running all species ####################### + # setup run for all species + mkdir /hive/data/genomes/hg38/bed/tba10way/consPhyloP/all + cd /hive/data/genomes/hg38/bed/tba10way/consPhyloP/all + rm -fr wigFix + mkdir wigFix + + gensub2 ../run.phyloP/ss.list single ../run.phyloP/template jobList + # beware overloading the cluster with these quick and high I/O jobs + para -ram=32g create jobList + para try ... check ... + para -maxJob=16 push + para time > run.time + +# Completed: 3308 of 3308 jobs +# CPU time in finished jobs: 647954s 10799.23m 179.99h 7.50d 0.021 y +# IO & Wait Time: 22374s 372.90m 6.22h 0.26d 0.001 y +# Average job time: 203s 3.38m 0.06h 0.00d +# Longest finished job: 349s 5.82m 0.10h 0.00d +# Submission to last job: 3226s 53.77m 0.90h 0.04d + + mkdir downloads + time for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` +do + echo "working: $D" 1>&2 + find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ + | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ + | gzip -c > downloads/${D}.phyloP10way.wigFix.gz +done + # real 48m50.219s + + du -hsc downloads + # 4.6G downloads + + # check integrity of data with wigToBigWig + time (zcat downloads/*.wigFix.gz \ + | wigToBigWig -verbose=2 stdin /hive/data/genomes/hg38/chrom.sizes \ + phyloP10way.bw) > bigWig.log 2>&1 + + + egrep "real|VmPeak" bigWig.log + # pid=66292: VmPeak: 33751268 kB + # real 43m40.194s + + + bigWigInfo phyloP10way.bw | sed -e 's/^/# /;' +# version: 4 +# isCompressed: yes +# isSwapped: 0 +# primaryDataSize: 6,304,076,591 +# primaryIndexSize: 93,404,704 +# zoomLevels: 10 +# chromCount: 355 +# basesCovered: 2,955,660,581 +# mean: 0.097833 +# min: -20.000000 +# max: 1.312000 +# std: 0.727453 + + # encode those files into wiggle data + time (zcat downloads/*.wigFix.gz \ + | wigEncode stdin phyloP10way.wig phyloP10way.wib) + +# Converted stdin, upper limit 1.31, lower limit -20.00 +# real 17m36.880s +# -rw-rw-r-- 1 2955660581 Nov 6 14:10 phyloP10way.wib +# -rw-rw-r-- 1 304274846 Nov 6 14:10 phyloP10way.wig + + du -hsc *.wi? + # 2.8G phyloP10way.wib + # 291M phyloP10way.wig + + # Load gbdb and database with wiggle. + ln -s `pwd`/phyloP10way.wib /gbdb/hg38/tba10way/phyloP10way.wib + time hgLoadWiggle -pathPrefix=/gbdb/hg38/tba10way hg38 \ + phyloP10way phyloP10way.wig + # real 0m30.538s + + # use to set trackDb.ra entries for wiggle min and max + # and verify table is loaded correctly + + wigTableStats.sh hg38 phyloP10way +# db.table min max mean count sumData +# hg38.phyloP10way -20 1.312 0.0978331 2955660581 2.89162e+08 +# stdDev viewLimits +# 0.727453 viewLimits=-3.53943:1.312 + + # that range is: 20+1.312= 21.312 for hBinSize=0.021312 + + # Create histogram to get an overview of all the data + time hgWiggle -doHistogram \ + -hBinSize=0.021312 -hBinCount=1000 -hMinVal=-20 -verbose=2 \ + -db=hg38 phyloP10way > histogram.data 2>&1 + # real 2m43.313s + + # xaxis range: + grep -v chrom histogram.data | grep "^[0-9]" | ave -col=2 stdin \ + | sed -e 's/^/# /;' +# Q1 -10.953050 +# median -6.861155 +# Q3 -2.769245 +# average -6.875971 +# min -20.000000 +# max 1.312000 +# count 768 +# total -5280.745380 +# standard deviation 4.757034 + + # find out the range for the 2:5 graph + grep -v chrom histogram.data | grep "^[0-9]" | ave -col=5 stdin \ + | sed -e 's/^/# /;' +# Q1 0.000000 +# median 0.000001 +# Q3 0.000140 +# average 0.001302 +# min 0.000000 +# max 0.023556 +# count 768 +# total 0.999975 +# standard deviation 0.003490 + + # create plot of histogram: + printf 'set terminal png small x000000 xffffff xc000ff x66ff66 xffff00 x00ffff font \ +"/usr/share/fonts/default/Type1/n022004l.pfb" +set size 1.4, 0.8 +set key left box +set grid noxtics +set grid ytics +set title " Human hg38 Histogram phyloP10way track" +set xlabel " phyloP10way score" +set ylabel " Relative Frequency" +set y2label " Cumulative Relative Frequency (CRF)" +set y2range [0:1] +set y2tics +set xrange [-5:1.5] +set yrange [0:0.04] + +plot "histogram.data" using 2:5 title " RelFreq" with impulses, \ + "histogram.data" using 2:7 axes x1y2 title " CRF" with lines +' | gnuplot > histo.png + + # verify it looks sane + display histo.png & + +############################################################################# +# construct download files for 30-way (TBD - 2015-04-15 - Hiram) + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons10way + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP10way + mkdir /hive/data/genomes/hg38/bed/tba10way/downloads + cd /hive/data/genomes/hg38/bed/tba10way/downloads + mkdir tba10way phastCons10way phyloP10way + + ######################################################################### + ## create upstream refGene maf files + cd /hive/data/genomes/hg38/bed/tba10way/downloads/tba10way + # bash script + +#!/bin/sh +export geneTbl="refGene" +for S in 300 2000 5000 +do + echo "making upstream${S}.maf" + featureBits hg38 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \ + | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \ + | /cluster/bin/$MACHTYPE/mafFrags hg38 tba10way \ + stdin stdout \ + -orgs=/hive/data/genomes/hg38/bed/tba10way/species.list \ + | gzip -c > upstream${S}.${geneTbl}.maf.gz + echo "done upstream${S}.${geneTbl}.maf.gz" +done + + # real 88m40.730s + +-rw-rw-r-- 1 52659159 Nov 6 11:46 upstream300.knownGene.maf.gz +-rw-rw-r-- 1 451126665 Nov 6 12:15 upstream2000.knownGene.maf.gz +-rw-rw-r-- 1 1080533794 Nov 6 12:55 upstream5000.knownGene.maf.gz + + ###################################################################### + ## compress the maf files + cd /hive/data/genomes/hg38/bed/tba10way/downloads/tba10way + mkdir maf + rsync -a -P ../../anno/result/ ./maf/ + du -hsc maf/ + # 156G maf + cd maf + time gzip *.maf & + # real 135m1.784s + + du -hscL maf ../../anno/result/ + # 18G maf + + cd maf + md5sum *.maf.gz *.nh > md5sum.txt + + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way/maf + cd maf + ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way/maf + cd -- + ln -s `pwd`/*.maf.gz `pwd`/*.nh `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way/ + + ########################################################################### + + cd /hive/data/genomes/hg38/bed/tba10way/downloads/tba10way + grep TREE ../../4d/all.mod | awk '{print $NF}' \ + | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > hg38.10way.nh + ~/kent/src/hg/utils/phyloTrees/commonNames.sh hg38.10way.nh \ + | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > hg38.10way.commonNames.nh + ~/kent/src/hg/utils/phyloTrees/scientificNames.sh hg38.10way.nh \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > hg38.10way.scientificNames.nh + time md5sum *.nh *.maf.gz > md5sum.txt + # real 0m3.147s + + ln -s `pwd`/*.maf.gz `pwd`/*.nh \ + /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way + + du -hsc ./maf ../../anno/result + # 18G ./maf + # 156G ../../anno/result + + # obtain the README.txt from hg38/multiz20way and update for this + # situation + ln -s `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/tba10way/ + + ##################################################################### + cd /hive/data/genomes/hg38/bed/tba10way/downloads/phastCons10way + + mkdir hg38.10way.phastCons + cd hg38.10way.phastCons + ln -s ../../../cons/all/downloads/*.wigFix.gz . + md5sum *.gz > md5sum.txt + + cd /hive/data/genomes/hg38/bed/tba10way/downloads/phastCons10way + ln -s ../../cons/all/phastCons10way.bw ./hg38.phastCons10way.bw + ln -s ../../cons/all/all.mod ./hg38.phastCons10way.mod + time md5sum *.mod *.bw > md5sum.txt + # real 0m20.354s + + # obtain the README.txt from hg38/phastCons20way and update for this + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons10way/hg38.10way.phastCons + cd hg38.10way.phastCons + ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons10way/hg38.10way.phastCons + + cd .. + # situation + ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons10way + + ##################################################################### + cd /hive/data/genomes/hg38/bed/tba10way/downloads/phyloP10way + + mkdir hg38.10way.phyloP + cd hg38.10way.phyloP + + ln -s ../../../consPhyloP/all/downloads/*.wigFix.gz . + md5sum *.wigFix.gz > md5sum.txt + + cd .. + + ln -s ../../consPhyloP/run.phyloP/all.mod hg38.phyloP10way.mod + ln -s ../../consPhyloP/all/phyloP10way.bw hg38.phyloP10way.bw + + md5sum *.mod *.bw > md5sum.txt + + # obtain the README.txt from hg38/phyloP20way and update for this + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP10way/hg38.10way.phyloP + cd hg38.10way.phyloP + ln -s `pwd`/* \ +/usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP10way/hg38.10way.phyloP + + cd .. + + # situation + ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP10way + +############################################################################# +# hgPal downloads (DONE - 2017-11-06 - Hiram) +# FASTA from 30-way for knownGene, refGene and knownCanonical + + ssh hgwdev + screen -S hg38HgPal + mkdir /hive/data/genomes/hg38/bed/tba10way/pal + cd /hive/data/genomes/hg38/bed/tba10way/pal + cat ../species.list | tr '[ ]' '[\n]' > order.list + + ### knownCanonical with full CDS + cd /hive/data/genomes/hg38/bed/tba10way/pal + export mz=tba10way + export gp=knownCanonical + export db=hg38 + mkdir exonAA exonNuc knownCanonical + + time cut -f1 ../../../chrom.sizes | while read C + do + echo $C 1>&2 + hgsql hg38 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$C'" > knownCanonical/$C.known.bed + done + + ls knownCanonical/*.known.bed | while read F + do + if [ -s $F ]; then + echo $F | sed -e 's#knownCanonical/##; s/.known.bed//' + fi + done | while read C + do + echo "date" + echo "mafGene -geneBeds=knownCanonical/$C.known.bed -noTrans $db $mz knownGene order.list stdout | \ + gzip -c > protNuc/$C.protNuc.fa.gz" + echo "mafGene -geneBeds=knownCanonical/$C.known.bed $db $mz knownGene order.list stdout | \ + gzip -c > protAA/$C.protAA.fa.gz" + done > $gp.$mz.prot.jobs + + time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1 + # 267m58.813s + + rm *.known.bed + export mz=tba10way + export gp=knownCanonical + export db=hg38 + zcat protAA/c*.gz | gzip -c > $gp.$mz.protAA.fa.gz & + zcat protNuc/c*.gz | gzip -c > $gp.$mz.protNuc.fa.gz & + # about 6 minutes + + ### knownCanonical broken up by exon + cd /hive/data/genomes/hg38/bed/multiz100way/pal + export mz=multiz100way + export gp=knownCanonical + export db=hg38 + mkdir exonAA exonNuc knownCanonical + + time cut -f1 ../../../chrom.sizes | while read C + do + echo $C 1>&2 + hgsql hg38 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$C'" > knownCanonical/$C.known.bed + done + # real 0m15.897s + + ls knownCanonical/*.known.bed | while read F + do + if [ -s $F ]; then + echo $F | sed -e 's#knownCanonical/##; s/.known.bed//' + fi + done | while read C + do + echo "date" + echo "mafGene -geneBeds=knownCanonical/$C.known.bed -exons -noTrans $db $mz knownGene order.list stdout | \ + gzip -c > exonNuc/$C.exonNuc.fa.gz" + echo "mafGene -geneBeds=knownCanonical/$C.known.bed -exons $db $mz knownGene order.list stdout | \ + gzip -c > exonAA/$C.exonAA.fa.gz" + done > $gp.$mz.jobs + + time sh -x $gp.$mz.jobs > $gp.$mz.job.log 2>&1 + # 267m58.813s + + rm *.known.bed + export mz=tba10way + export gp=knownCanonical + export db=hg38 + zcat exonAA/c*.gz | gzip -c > $gp.$mz.exonAA.fa.gz & + zcat exonNuc/c*.gz | gzip -c > $gp.$mz.exonNuc.fa.gz & + # about 6 minutes + + rm -rf exonAA exonNuc + + export mz=multiz100way + export gp=knownCanonical + export db=hg38 + export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments + mkdir -p $pd + ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz + ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz + ln -s `pwd`/$gp.$mz.protAA.fa.gz $pd/$gp.protAA.fa.gz + ln -s `pwd`/$gp.$mz.protNuc.fa.gz $pd/$gp.protNuc.fa.gz + cd $pd + md5sum *.fa.gz > md5sum.txt + + rm -rf exonAA exonNuc + + export mz=tba10way + export gp=knownCanonical + export db=hg38 + export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments + mkdir -p $pd + ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz + ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz + + # knownGene + export mz=tba10way + export gp=knownGene + export db=hg38 + export I=0 + export D=0 + mkdir exonAA exonNuc + for C in `sort -nk2 ../../../chrom.sizes | cut -f1` + do + I=`echo $I | awk '{print $1+1}'` + D=`echo $D | awk '{print $1+1}'` + dNum=`echo $D | awk '{printf "%03d", int($1/300)}'` + mkdir -p exonNuc/${dNum} > /dev/null + mkdir -p exonAA/${dNum} > /dev/null + echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/${dNum}/$C.exonNuc.fa.gz &" + echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/${dNum}/$C.exonAA.fa.gz &" + if [ $I -gt 16 ]; then + echo "date" + echo "wait" + I=0 + fi + done > $gp.jobs + echo "date" >> $gp.jobs + echo "wait" >> $gp.jobs + + time (sh -x ./$gp.jobs) > $gp.jobs.log 2>&1 + # real 79m18.323s + + export mz=tba10way + export gp=knownGene + time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \ + | gzip -c > $gp.$mz.exonAA.fa.gz + # real 1m28.841s + + time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \ + | gzip -c > $gp.$mz.exonNuc.fa.gz + # real 3m56.370s + + # -rw-rw-r-- 1 397928833 Nov 6 18:44 knownGene.tba10way.exonAA.fa.gz + # -rw-rw-r-- 1 580377720 Nov 6 18:49 knownGene.tba10way.exonNuc.fa.gz + + export mz=tba10way + export gp=knownGene + export db=hg38 + export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments + mkdir -p $pd + ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz + ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz + ln -s `pwd`/md5sum.txt $pd/ + + cd $pd + md5sum *.fa.gz > md5sum.txt + + rm -rf exonAA exonNuc + +############################################################################# +# wiki page for 30-way (DONE - 2017-11-06 - Hiram) + mkdir /hive/users/hiram/bigWays/hg38.10way + cd /hive/users/hiram/bigWays + echo "hg38" > hg38.10way/ordered.list + awk '{print $1}' /hive/data/genomes/hg38/bed/tba10way/10way.distances.txt \ + >> hg38.10way/ordered.list + + # sizeStats.sh catches up the cached measurements required for data + # in the tables. They are usually already mostly done, only new + # assemblies will have updates. + ./sizeStats.sh hg38.10way/ordered.list + # dbDb.sh constructs hg38.10way/XenTro9_30-way_conservation_alignment.html + # may need to add new assembly references to srcReference.list and + # urlReference.list + ./dbDb.sh hg38 10way + # sizeStats.pl constructs hg38.10way/XenTro9_30-way_Genome_size_statistics.html + # this requires entries in coverage.list for new sequences + ./sizeStats.pl hg38 10way + + # defCheck.pl constructs XenTro9_30-way_conservation_lastz_parameters.html + ./defCheck.pl hg38 10way + + # this constructs the html pages in hg38.10way/: +# -rw-rw-r-- 1 6247 May 2 17:07 XenTro9_30-way_conservation_alignment.html +# -rw-rw-r-- 1 8430 May 2 17:09 XenTro9_30-way_Genome_size_statistics.html +# -rw-rw-r-- 1 5033 May 2 17:10 XenTro9_30-way_conservation_lastz_parameters.html + + # add those pages to the genomewiki. Their page names are the + # names of the .html files without the .html: +# XenTro9_30-way_conservation_alignment +# XenTro9_30-way_Genome_size_statistics +# XenTro9_30-way_conservation_lastz_parameters + + # when you view the first one you enter, it will have links to the + # missing two. + +############################################################################ +# pushQ readmine (DONE - 2017-11-07 - Hiram) + + cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg38 + find -L `pwd`/tba10way `pwd`/phastCons10way `pwd`/phyloP10way \ + /gbdb/hg38/tba10way -type f \ + > /hive/data/genomes/hg38/bed/tba10way/downloads/redmine.20216.fileList + wc -l /hive/data/genomes/hg38/bed/tba10way/downloads/redmine.20216.fileList +# 1450 /hive/data/genomes/hg38/bed/tba10way/downloads/redmine.20216.fileList + + cd /hive/data/genomes/hg38/bed/tba10way/downloads + hgsql -e 'show tables;' hg38 | grep 10way \ + | sed -e 's/^/hg38./;' > redmine.20216.table.list + +############################################################################