3c614c8b6f65a275dec519d292b870afeec12335 hiram Sat Dec 19 09:07:59 2020 -0800 multiz done running up iRows refs #26584 diff --git src/hg/makeDb/doc/mm39/multiz35way.txt src/hg/makeDb/doc/mm39/multiz35way.txt new file mode 100644 index 0000000..30abe82 --- /dev/null +++ src/hg/makeDb/doc/mm39/multiz35way.txt @@ -0,0 +1,2250 @@ +############################################################################# +## 35-Way Multiz (TBD - 2020-12-16 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/mm39/bed/multiz35way + cd /hive/data/genomes/mm39/bed/multiz35way + + # from the 220-way in the source tree, select out the 35 used here: + /cluster/bin/phast/tree_doctor \ + --prune-all-but bosTau9,calJac4,canFam4,criGri1,casCan1,cavPor3,danRer11,echTel2,equCab3,eriEur2,galGal6,galVar1,gorGor6,hg38,loxAfr3,manPen1,mm39,monDom5,neoSch1,ochPri3,oryCun2,otoGar3,oviAri4,panPan3,panTro6,petMar3,rheMac10,rn6,sorAra2,speTri2,susScr3,tarSyr2,tupBel1,turTru2,xenTro9 \ + /cluster/home/hiram/kent/src/hg/utils/phyloTrees/220way.nh \ + | sed -e 's/criGri1/GCF_003668045.3/;' \ + > t0.nh + + # using TreeGraph2 tree editor on the Mac, rearrange to get mm39 + # at the top, and attempt to get the others in phylo order: + /cluster/bin/phast/all_dists t.nh | grep mm39 \ + | sed -e "s/mm39.//" | sort -k2n | sed -e 's/^/#\t/;' +# rn6 0.186098 +# GCF_003668045.3 0.332282 +# casCan1 0.412432 +# speTri2 0.417900 +# manPen1 0.485701 +# cavPor3 0.491203 +# galVar1 0.493420 +# calJac4 0.494237 +# gorGor6 0.500585 +# hg38 0.502391 +# panPan3 0.502461 +# panTro6 0.502681 +# tarSyr2 0.503897 +# rheMac10 0.510018 +# otoGar3 0.511897 +# equCab3 0.520098 +# turTru2 0.540150 +# canFam4 0.543004 +# tupBel1 0.549623 +# susScr3 0.549974 +# loxAfr3 0.556386 +# oryCun2 0.556860 +# oviAri4 0.574054 +# neoSch1 0.585546 +# bosTau9 0.599054 +# ochPri3 0.643702 +# eriEur2 0.676481 +# echTel2 0.703393 +# sorAra2 0.724258 +# monDom5 0.921254 +# xenTro9 1.214580 +# galGal6 1.326078 +# petMar3 2.253737 +# danRer11 2.279062 + + # what that looks like: +~/kent/src/hg/utils/phyloTrees/asciiTree.pl t.nh > mm39.35way.nh +~/kent/src/hg/utils/phyloTrees/asciiTree.pl mm39.35way.nh | sed -e 's/^/# /;' + +# ((((((((((((((mm39:0.089509, +# rn6:0.096589):0.072773, +# GCF_003668045.3:0.17):0.08015, +# casCan1:0.17):0.05, +# speTri2:0.125468):0.022992, +# cavPor3:0.175779):0.025746, +# (oryCun2:0.114227, +# ochPri3:0.201069):0.101463):0.015313, +# ((((((((hg38:0.00655, +# panTro6:0.00684):0.00122, +# panPan3:0.00784):0.003, +# gorGor6:0.008964):0.025204, +# rheMac10:0.043601):0.02183, +# calJac4:0.04965):0.05209, +# tarSyr2:0.1114):0.02052, +# otoGar3:0.13992):0.013494, +# (tupBel1:0.136203, +# galVar1:0.08):0.054937):0.002):0.020593, +# (((susScr3:0.12, +# (turTru2:0.064688, +# (bosTau9:0.11, +# oviAri4:0.085):0.013592):0.045488):0.02, +# ((equCab3:0.084397, +# manPen1:0.05):0.017, +# (canFam4:0.054458, +# neoSch1:0.097):0.069845):0.008727):0.011671, +# (eriEur2:0.221785, +# sorAra2:0.269562):0.056393):0.021227):0.023664, +# (loxAfr3:0.098929, +# echTel2:0.245936):0.056717):0.234728, +# monDom5:0.285786):0.181168, +# galGal6:0.509442):0.05, +# xenTro9:0.347944):0.211354, +# danRer11:1.201072):0.2, +# petMar3:0.975747); + + # extract species list from that .nh file + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + mm39.35way.nh | xargs echo | sed 's/ //g; s/,/ /g' \ + | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt + + # construct db to name translation list: + cat species.list.txt | while read DB +do +hgsql -N -e "select name,organism from dbDb where name=\"${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. Crab-eating -> Crab_eating, +# the Crab-eating didn't survive the tree_doctor + +/cluster/bin/phast/tree_doctor --rename "`cat db.to.name.txt`" mm39.35way.nh \ + | sed -e 's/0\+)/)/g; s/0\+,/,/g' \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + | sed -e "s#_x_#'#g;" > mm39.35way.commonNames.nh + + cat mm39.35way.commonNames.nh | sed -e 's/^/# /;' +# ((((((((((((Human:0.00655, +# Chimp:0.00684):0.00122, +# Bonobo:0.00784):0.003, +# Gorilla:0.008964):0.009693, +# Orangutan:0.01894):0.003471, +# Gibbon:0.02227):0.01204, +# (((((Rhesus:0.003991, +# (Crab_eating_macaque:0.002991, +# Pig_tailed_macaque:0.005):0.001):0.001, +# Sooty_mangabey:0.008):0.005, +# Baboon:0.010042):0.01061, +# (Green_monkey:0.027, +# Drill:0.03):0.002):0.003, +# ((Proboscis_monkey:0.0007, +# Angolan_colobus:0.0008):0.0008, +# (Golden_snub:0.0007, +# Black_snub:0.0007):0.0008):0.018):0.02):0.02183, +# (((Marmoset:0.03, +# Squirrel_monkey:0.01035):0.00865, +# White_faced_sapajou:0.04):0.006, +# Ma's_night_monkey:0.04):0.005):0.05209, +# Tarsier:0.1114):0.02052, +# (((Mouse_lemur:0.0556, +# Coquerel's_sifaka:0.05):0.015, +# (Black_lemur:0.01, +# Sclater's_lemur:0.01):0.015):0.015, +# Bushbaby:0.1194):0.02052):0.015494, +# Mouse:0.356483):0.020593, +# Dog:0.165928):0.023664, +# Armadillo:0.176526); + +# 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/mm39_35way.png + + ~/kent/src/hg/utils/phyloTrees/asciiTree.pl mm39.35way.nh > t.nh + ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > mm39.35way.scientificNames.nh + rm -f t.nh + cat mm39.35way.scientificNames.nh | sed -e 's/^/# /;' +# ((((((((((((Homo_sapiens:0.00655, +# Pan_troglodytes:0.00684):0.00122, +# Pan_paniscus:0.00784):0.003, +# Gorilla_gorilla_gorilla:0.008964):0.009693, +# Pongo_pygmaeus_abelii:0.01894):0.003471, +# Nomascus_leucogenys:0.02227):0.01204, +# (((((Macaca_mulatta:0.003991, +# (Macaca_fascicularis:0.002991, +# Macaca_nemestrina:0.005):0.001):0.001, +# Cercocebus_atys:0.008):0.005, +# Papio_anubis:0.010042):0.01061, +# (Chlorocebus_sabaeus:0.027, +# Mandrillus_leucophaeus:0.03):0.002):0.003, +# ((Nasalis_larvatus:0.0007, +# Colobus_angolensis_palliatus:0.0008):0.0008, +# (Rhinopithecus_roxellana:0.0007, +# Rhinopithecus_bieti:0.0007):0.0008):0.018):0.02):0.02183, +# (((Callithrix_jacchus:0.03, +# Saimiri_boliviensis:0.01035):0.00865, +# Cebus_capucinus_imitator:0.04):0.006, +# Aotus_nancymaae:0.04):0.005):0.05209, +# Tarsius_syrichta:0.1114):0.02052, +# (((Microcebus_murinus:0.0556, +# Propithecus_coquereli:0.05):0.015, +# (Eulemur_macaco:0.01, +# Eulemur_flavifrons:0.01):0.015):0.015, +# Otolemur_garnettii:0.1194):0.02052):0.015494, +# Mus_musculus:0.356483):0.020593, +# Canis_lupus_familiaris:0.165928):0.023664, +# Dasypus_novemcinctus:0.176526); + + /cluster/bin/phast/all_dists mm39.35way.nh | grep mm39 \ + | sed -e "s/mm39.//" | sort -k2n > 35way.distances.txt + # Use this output to create the table below + cat 35way.distances.txt | sed -e 's/^/# /;' +# rn6 0.186098 +# GCF_003668045.3 0.332282 +# casCan1 0.412432 +# speTri2 0.417900 +# manPen1 0.485701 +# cavPor3 0.491203 +# galVar1 0.493420 +# calJac4 0.494237 +# gorGor6 0.500585 +# hg38 0.502391 +# panPan3 0.502461 +# panTro6 0.502681 +# tarSyr2 0.503897 +# rheMac10 0.510018 +# otoGar3 0.511897 +# equCab3 0.520098 +# turTru2 0.540150 +# canFam4 0.543004 +# tupBel1 0.549623 +# susScr3 0.549974 +# loxAfr3 0.556386 +# oryCun2 0.556860 +# oviAri4 0.574054 +# neoSch1 0.585546 +# bosTau9 0.599054 +# ochPri3 0.643702 +# eriEur2 0.676481 +# echTel2 0.703393 +# sorAra2 0.724258 +# monDom5 0.921254 +# xenTro9 1.214580 +# galGal6 1.326078 +# petMar3 2.253737 +# danRer11 2.279062 + + printf '#!/usr/bin/env perl + +use strict; +use warnings; + +open (FH, "<35way.distances.txt") or + die "can not read 35way.distances.txt"; + +my $count = 0; +while (my $line = <FH>) { + chomp $line; + my ($D, $dist) = split('"'"'\\s+'"'"', $line); + my $chain = "chain" . ucfirst($D); + my $B="/hive/data/genomes/mm39/bed/lastz.$D/fb.mm39." . + $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.mm39/fb.${D}.chainMm39Link.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 +# count phylo chain synNet rBest synNet v. query +# dist link chain +# 001 0.1861 (% 70.901) (% 66.256) (% 65.494) 6.55 - Rat rn6 +# 002 0.3323 (% 58.000) (% 54.406) (% 00.000) 6.20 - Cricetulus griseus GCF_003668045.3 +# 003 0.4124 (% 36.600) (% 32.404) (% 34.407) 11.46 - Beaver casCan1 +# 004 0.4179 (% 34.147) (% 31.953) (% 32.373) 6.43 - Squirrel speTri2 +# 005 0.4857 (% 27.322) (% 22.622) (% 25.847) 17.20 - Chinese pangolin manPen1 +# 006 0.4912 (% 28.378) (% 26.311) (% 26.932) 7.28 - Guinea pig cavPor3 +# 007 0.4934 (% 35.714) (% 31.386) (% 33.751) 12.12 - Malayan flying lemur galVar1 +# 008 0.4942 (% 33.090) (% 31.297) (% 31.492) 5.42 - Marmoset calJac4 +# 009 0.5006 (% 35.064) (% 33.225) (% 33.360) 5.24 - Gorilla gorGor6 +# 010 0.5024 (% 35.372) (% 33.566) (% 33.646) 5.11 - Human hg38 +# 011 0.5025 (% 35.282) (% 33.492) (% 33.579) 5.07 - Bonobo panPan3 +# 012 0.5027 (% 35.291) (% 33.511) (% 33.608) 5.04 - Chimp panTro6 +# 013 0.5039 (% 32.278) (% 28.908) (% 30.629) 10.44 - Tarsier tarSyr2 +# 014 0.5100 (% 34.838) (% 33.095) (% 33.167) 5.00 - Rhesus rheMac10 +# 015 0.5119 (% 29.729) (% 27.878) (% 28.263) 6.23 - Bushbaby otoGar3 +# 016 0.5201 (% 34.831) (% 33.041) (% 33.077) 5.14 - Horse equCab3 +# 017 0.5402 (% 30.188) (% 24.901) (% 28.769) 17.51 - Dolphin turTru2 +# 018 0.5430 (% 29.376) (% 27.756) (% 27.951) 5.51 - Dog canFam4 +# 019 0.5496 (% 19.691) (% 12.280) (% 18.365) 37.64 - Tree shrew tupBel1 +# 020 0.5500 (% 25.611) (% 23.252) (% 24.292) 9.21 - Pig susScr3 +# 021 0.5564 (% 25.756) (% 23.827) (% 24.416) 7.49 - Elephant loxAfr3 +# 022 0.5569 (% 25.182) (% 23.079) (% 23.777) 8.35 - Rabbit oryCun2 +# 023 0.5741 (% 26.200) (% 24.360) (% 24.783) 7.02 - Sheep oviAri4 +# 024 0.5855 (% 31.257) (% 29.478) (% 29.730) 5.69 - Hawaiian monk seal neoSch1 +# 025 0.5991 (% 26.588) (% 24.846) (% 25.188) 6.55 - Cow bosTau9 +# 026 0.6437 (% 18.559) (% 16.419) (% 17.355) 11.53 - Pika ochPri3 +# 027 0.6765 (% 13.450) (% 09.501) (% 12.323) 29.36 - Hedgehog eriEur2 +# 028 0.7034 (% 14.456) (% 11.161) (% 13.329) 22.79 - Tenrec echTel2 +# 029 0.7243 (% 13.370) (% 10.430) (% 12.301) 21.99 - Shrew sorAra2 +# 030 0.9213 (% 05.382) (% 04.390) (% 04.627) 18.43 - Opossum monDom5 +# 031 1.2146 (% 01.936) (% 00.783) (% 01.354) 59.56 - X. tropicalis xenTro9 +# 032 1.3261 (% 02.537) (% 01.835) (% 02.015) 27.67 - Chicken galGal6 +# 033 2.2537 (% 00.905) (% 00.027) (% 00.517) 97.02 - Lamprey petMar3 +# 034 2.2791 (% 01.416) (% 00.185) (% 00.947) 86.94 - Zebrafish danRer11 +# count phylo chain synNet rBest synNet v. query +# dist link chain + +# 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' \ + mm39.35way.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/^/# /;' +# mm39 rn6 GCF_003668045.3 casCan1 speTri2 cavPor3 oryCun2 ochPri3 hg38 +# panTro6 panPan3 gorGor6 rheMac10 calJac4 tarSyr2 otoGar3 tupBel1 galVar1 +# susScr3 turTru2 bosTau9 oviAri4 equCab3 manPen1 canFam4 neoSch1 eriEur2 +# sorAra2 loxAfr3 echTel2 monDom5 galGal6 xenTro9 danRer11 petMar3 + + # bash shell syntax here ... + cd /hive/data/genomes/mm39/bed/multiz35way + + export H=/hive/data/genomes/mm39/bed + mkdir mafLinks + # good, phylo close assemblies can use syntenic net: + for G in rn6 cavPor3 calJac4 gorGor6 hg38 panPan3 panTro6 rheMac10 \ + equCab3 canFam4 oviAri4 neoSch1 + do + cd $H/multiz35way + rm -fr mafLinks/$G + mkdir mafLinks/$G + cd mafLinks/$G + mafSplit -outDirDepth=0 -byTarget -useFullSequenceName \ + /dev/null . ${H}/lastz.$G/axtChain/mm39.${G}.synNet.maf.gz + gzip *.maf + echo lastz.$G/axtChain/mm39.${G}.synNet.maf.gz + done + + # GCF_003668045.3 is special and was done with a name translation step + # to eliminate dots in the assembly name and in the sequence names + # maf files expect only one dot on the s lines: assembly.sequence + mkdir mafLinks/GCF_003668045v3 + cd mafLinks/GCF_003668045v3 + mafSplit -outDirDepth=0 -byTarget -useFullSequenceName \ + /dev/null . ../../translated/GCF_003668045v3.maf.gz + gzip *.maf + + # assemblies using recip best net: + for G in casCan1 speTri2 manPen1 tarSyr2 otoGar3 turTru2 tupBel1 \ + susScr3 loxAfr3 oryCun2 bosTau9 ochPri3 eriEur2 echTel2 sorAra2 + do + cd $H/multiz35way + rm -fr mafLinks/$G + mkdir mafLinks/$G + cd mafLinks/$G + echo ln -s "lastz.$G/mafRBestNet/"'*' ./mafLinks/$G + ln -s ${H}/lastz.$G/mafRBestNet/*.maf.gz ./ + done + + # and finally, assemblies using the base mafNet + for G in galVar1 monDom5 xenTro9 galGal6 danRer11 petMar3 + do + cd $H/multiz35way + rm -fr mafLinks/$G + mkdir mafLinks/$G + cd mafLinks/$G + echo ln -s "lastz.$G/mafNet/"'*' ./mafLinks/$G + ln -s ${H}/lastz.$G/mafNet/*.maf.gz ./ + done + # verify the symLinks are good, should be 22 primary chromosomes for all: + for D in `ls -d mafLinks/*` + do + printf "%02d\t%s\n" "`ls $D | egrep -v "chrUn|random" | wc -l`" "${D}" + done | sed -e 's/^/#\t/;' +# 22 mafLinks/GCF_003668045.3 +# 22 mafLinks/bosTau9 +# 22 mafLinks/calJac4 +... +# 22 mafLinks/tupBel1 +# 22 mafLinks/turTru2 +# 22 mafLinks/xenTro9 + + # verify the symLinks are good, various other numbers with all chromosomes: + for D in `ls -d mafLinks/*` + do + printf "%02d\t%s\n" "`ls $D | wc -l`" "${D}" + done | sed -e 's/^/#\t/;' | sort -k2,2n +# 25 mafLinks/cavPor3 +# 25 mafLinks/oviAri4 +# 27 mafLinks/canFam4 +... +# 47 mafLinks/speTri2 +# 49 mafLinks/rn6 +# 54 mafLinks/galVar1 + + # Interesting that there are no matches to all the chromosomes by + # any organism. Let's see how many if all are placed together + for D in `ls -d mafLinks/*` + do + ls $D | grep chr | sed -e 's#.*/##;' + done | sort -u | wc -l +# 54 + # seems to be the limit, wonder what is missing: + find ./mafLinks -type f | sed -e 's#.*/##;' \ + | sed -e 's/.maf.gz//;' | sort -u > maf.list.here + comm -23 <(cut -f1 ../../chrom.sizes | sort ) maf.list.here | sed -e 's/^/#\t/;' +# chr1_GL456239v1_random +# chr4_JH584295v1_random +# chrUn_GL456368v1 +# chrUn_GL456370v1 +# chrUn_GL456383v1 +# chrUn_GL456389v1 +# chrUn_GL456390v1 +# chrUn_GL456392v1 +# chrUn_GL456396v1 +# chrUn_MU069435v1 + + # and the sizes of those missed chroms: + comm -23 <(cut -f1 ../../chrom.sizes | sort ) maf.list.here \ +| while read S; do grep "${S}" ../../chrom.sizes; done | sed -e 's/^/#\t/;' +# chr1_GL456239v1_random 40056 +# chr4_JH584295v1_random 1976 +# chrUn_GL456368v1 20208 +# chrUn_GL456370v1 26764 +# chrUn_GL456383v1 38659 +# chrUn_GL456389v1 28772 +# chrUn_GL456390v1 24668 +# chrUn_GL456392v1 23629 +# chrUn_GL456396v1 21240 +# chrUn_MU069435v1 31129 + +XXX + # try to do these as full chromosomes without the splitting procedure + + mkdir /hive/data/genomes/mm39/bed/multiz35way/fullChromRun + cd /hive/data/genomes/mm39/bed/multiz35way/fullChromRun + 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 + + find ../../mafLinks -type l | grep ".maf.gz$" | xargs -L 1 basename \ + | sed -e 's/.gz//;' | sort -u > maf.list + + wc -l maf.list + # 54 maf.list + + # set the db and pairs directories here + cat > autoMultiz.csh << '_EOF_' +#!/bin/csh -ef +set db = mm39 +set c = $1 +set result = $2 +set run = `/bin/pwd` +set tmp = /dev/shm/$db/multiz.$c +set pairs = /hive/data/genomes/mm39/bed/multiz35way/mafLinks +/bin/rm -fr $tmp +/bin/mkdir -p $tmp +/usr/bin/sed -e 's/GCF_003668045.3/GCF_003668045v3/;' ../../tree.nh > $tmp/tree.nh +/usr/bin/sed -e 's/GCF_003668045.3/GCF_003668045v3/;' ../../species.list > $tmp/species.list +pushd $tmp > /dev/null +foreach s (`/bin/sed -e "s/$db //" species.list`) + set in = $pairs/$s/$c + set out = $db.$s.sing.maf + if (-e $in.gz) then + /bin/zcat $in.gz > $out + if (! -s $out) then + echo "##maf version=1 scoring=autoMZ" > $out + endif + else if (-e $in) then + /bin/ln -s $in $out + else + echo "##maf version=1 scoring=autoMZ" > $out + endif +end +set path = ($run/penn $path); rehash +$run/penn/autoMZ + T=$tmp E=$db "`cat tree.nh`" $db.*.sing.maf $c \ + > /dev/null +popd > /dev/null +/bin/rm -f $result +/bin/cp -p $tmp/$c $result +/bin/rm -fr $tmp +'_EOF_' +# << happy emacs + chmod +x autoMultiz.csh + + printf '#LOOP +./autoMultiz.csh $(file1) {check out line+ /hive/data/genomes/mm39/bed/multiz35way/fullChromRun/maf/$(root1).maf} +#ENDLOOP +' > template + + ssh ku + cd /hive/data/genomes/mm39/bed/multiz35way/fullChromRun/run + gensub2 maf.list single template jobList + para -ram=64g create jobList +# Completed: 7 of 7 jobs +# CPU time in finished jobs: 295337s 4922.28m 82.04h 3.42d 0.009 y +# IO & Wait Time: 226s 3.77m 0.06h 0.00d 0.000 y +# Average job time: 42223s 703.72m 11.73h 0.49d +# Longest finished job: 58035s 967.25m 16.12h 0.67d +# Submission to last job: 58046s 967.43m 16.12h 0.67d + + + # need to split these things up into smaller pieces for + # efficient kluster run. + mkdir /hive/data/genomes/mm39/bed/multiz35way/mafSplit + cd /hive/data/genomes/mm39/bed/multiz35way/mafSplit + + # mafSplitPos splits on gaps or repeat areas that will not have + # any chains, approx 5 Mbp intervals, gaps at least 10,000 + mafSplitPos -minGap=10000 mm39 5 stdout | sort -u \ + | sort -k1,1 -k2,2n > mafSplit.bed + # see also multiz35way.txt for more discussion of this procedure + + # run a kluster job to split them all + ssh ku + cd /hive/data/genomes/mm39/bed/multiz35way/mafSplit + + printf ' +#!/bin/csh -ef +set G = $1 +set M = $2 +mkdir -p $G +pushd $G > /dev/null +if ( -s mm39_${M}.00.maf ) then + /bin/rm -f mm39_${M}.*.maf +endif +/cluster/bin/x86_64/mafSplit ../mafSplit.bed mm39_ ../../mafLinks/${G}/${M}.maf.gz +/bin/gzip mm39_*.maf +popd > /dev/null +' > runOne + + # << happy emacs + chmod +x runOne + + printf '#LOOP +runOne $(dir1) $(file1) {check out exists+ $(dir1)/mm39_chr1.00.maf.gz} +#ENDLOOP +' > template + + find ../mafLinks -type l | awk -F'/' '{printf "%s/%s\n", $3,$4}' \ + | sed -e 's/.maf.gz//;' > maf.list + + gensub2 maf.list single template jobList + para -ram=16g create jobList + para try ... check ... push ... etc... +# Completed: 29 of 29 jobs +# CPU time in finished jobs: 31855s 530.92m 8.85h 0.37d 0.001 y +# IO & Wait Time: 0s 0.00m 0.00h 0.00d 0.000 y +# Average job time: 1070s 17.84m 0.30h 0.01d +# Longest finished job: 1544s 25.73m 0.43h 0.02d +# Submission to last job: 3302s 55.03m 0.92h 0.04d + + # construct a list of all possible maf file names. + # they do not all exist in each of the species directories + find . -type f | grep "maf.gz" | wc -l + # 16567 + + find . -type f | grep ".maf.gz$" | xargs -L 1 basename | sort -u \ + > run.maf.list + wc -l run.maf.list + # 678 run.maf.list + + # number of chroms with data: + awk -F'.' '{print $1}' run.maf.list | sed -e 's/mm39_//;' \ + | sort | uniq -c | sort -n | wc -l + # 358 + + mkdir /hive/data/genomes/mm39/bed/multiz35way/splitRun + cd /hive/data/genomes/mm39/bed/multiz35way/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 = mm39 +set c = $1 +set result = $2 +set run = `/bin/pwd` +set tmp = /dev/shm/$db/multiz.$c +set pairs = /hive/data/genomes/mm39/bed/multiz35way/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 $(root1) {check out line+ /hive/data/genomes/mm39/bed/multiz35way/splitRun/maf/$(root1)} +#ENDLOOP +' > template + + ln -s ../../mafSplit/run.maf.list maf.list + + ssh ku + cd /hive/data/genomes/mm39/bed/multiz35way/splitRun/run + gensub2 maf.list single template jobList + para create jobList + para try ... check ... push ... etc... +# Completed: 678 of 678 jobs +# CPU time in finished jobs: 3849518s 64158.63m 1069.31h 44.55d 0.122 y +# IO & Wait Time: 4040s 67.33m 1.12h 0.05d 0.000 y +# Average job time: 5684s 94.73m 1.58h 0.07d +# Longest finished job: 37569s 626.15m 10.44h 0.43d +# Submission to last job: 79158s 1319.30m 21.99h 0.92d + + # put the split maf results back together into a single per-chrom maf file + # eliminate duplicate comments + ssh hgwdev + cd /hive/data/genomes/mm39/bed/multiz35way/splitRun + mkdir ../maf + # no need to save the comments since they are lost with mafAddIRows + + cat << '_EOF_' >> runOne +#!/bin/csh -fe +set C = $1 +if ( -s ../maf/${C}.maf.gz ) then + rm -f ../maf/${C}.maf.gz +endif +if ( -s maf/mm39_${C}.00.maf ) then + head -q -n 1 maf/mm39_${C}.00.maf | sort -u > ../maf/${C}.maf + grep -h -v "^#" `ls maf/mm39_${C}.*.maf | sort -t. -k2,2n` >> ../maf/${C}.maf + tail -q -n 1 maf/mm39_${C}.00.maf | sort -u >> ../maf/${C}.maf +else + touch ../maf/${C}.maf +endif +'_EOF_' + # << happy emacs + chmod +x runOne + + cat << '_EOF_' >> template +#LOOP +runOne $(root1) {check out exists ../maf/$(root1).maf} +#ENDLOOP +'_EOF_' + # << happy emacs + + cut -f1 ../../../chrom.sizes > chr.list + ssh ku + cd /hive/data/genomes/mm39/bed/multiz35way/splitRun + gensub2 chr.list single template jobList + para -ram=16g create jobList + para try ... check ... push ... etc ... + para -maxJob=32 push +# Completed: 455 of 455 jobs +# CPU time in finished jobs: 265s 4.42m 0.07h 0.00d 0.000 y +# IO & Wait Time: 1472s 24.53m 0.41h 0.02d 0.000 y +# Average job time: 4s 0.06m 0.00h 0.00d +# Longest finished job: 52s 0.87m 0.01h 0.00d +# Submission to last job: 92s 1.53m 0.03h 0.00d + + cd /hive/data/genomes/mm39/bed/multiz35way/maf + # 97 of them have empty results, they have to be removed + ls -ogrt | awk '$3 == 0' | awk '{print $NF}' | xargs rm -f + + + # Load into database + mkdir -p /gbdb/mm39/multiz35way/maf + cd /hive/data/genomes/mm39/bed/multiz35way/maf + ln -s `pwd`/*.maf /gbdb/mm39/multiz35way/maf/ + + # this generates an immense multiz35way.tab file in the directory + # where it is running. Best to run this over in scratch. + # This is going to take all day. + cd /dev/shm + time hgLoadMaf -pathPrefix=/gbdb/mm39/multiz35way/maf mm39 multiz35way + # Loaded 40625470 mafs in 358 files from /gbdb/mm39/multiz35way/maf + # real 28m23.045s + + time (cat /gbdb/mm39/multiz35way/maf/*.maf \ + | hgLoadMafSummary -verbose=2 -minSize=30000 \ + -mergeGap=1500 -maxSize=200000 mm39 multiz35waySummary stdin) +# Created 4568973 summary blocks from 850984320 components and 40625470 mafs from stdin +# real 49m52.561s + + +-rw-rw-r-- 1 2171190193 Nov 2 16:40 multiz35way.tab +-rw-rw-r-- 1 215756735 Nov 2 17:44 multiz35waySummary.tab + + wc -l multiz30*.tab +# 40625470 multiz35way.tab +# 4568973 multiz35waySummary.tab + + rm multiz35way*.tab + +####################################################################### +# GAP ANNOTATE MULTIZ30WAY MAF AND LOAD TABLES (TBD - 2017-11-03 - Hiram) + # mafAddIRows has to be run on single chromosome maf files, it does not + # function correctly when more than one reference sequence + # are in a single file. + mkdir -p /hive/data/genomes/mm39/bed/multiz35way/anno + cd /hive/data/genomes/mm39/bed/multiz35way/anno + + # check for N.bed files everywhere: + for DB in `sed -e 's/ GCF_003668045.3//;' ../species.list` +do + if [ ! -s /hive/data/genomes/${DB}/${DB}.N.bed ]; then + echo "MISS: ${DB}" +# cd /hive/data/genomes/${DB} +# twoBitInfo -nBed ${DB}.2bit ${DB}.N.bed + else + echo " OK: ${DB}" + fi + cd /hive/data/genomes/mm39/bed/multiz35way/anno +done + twoBitInfo -nBed \ +/hive/data/genomes/asmHubs/refseqBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/GCF_003668045.3_CriGri-PICRH-1.0.2bit \ +stdout | sed -e 's/\./v/g;' > GCF_003668045v3.bed + sed -e 's/\./v/g;' /hive/data/genomes/asmHubs/refseqBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/GCF_003668045.3_CriGri-PICRH-1.0.chrom.sizes \ + > GCF_003668045v3.len + + cd /hive/data/genomes/mm39/bed/multiz35way/anno + for DB in `sed -e 's/ GCF_003668045.3//;' ../species.list` +do + echo "${DB} " + ln -s /hive/data/genomes/${DB}/${DB}.N.bed ${DB}.bed + ln -s /hive/data/genomes/${DB}/chrom.sizes ${DB}.len +done + ls *.bed > nBeds + ls *.len > sizes + # make sure they all are successful symLinks: + ls -ogrtL *.bed | wc -l + # 35 + ls -ogrtL *.len | wc -l + # 35 + wc -l nBeds sizes + # 35 nBeds + # 35 sizes + + screen -S mm39 # use a screen to control this longish job + # do not need to go to ku for this, can run on hgwdev parasol + cd /hive/data/genomes/mm39/bed/multiz35way/anno + mkdir result + + printf '#LOOP +mafAddIRows -nBeds=nBeds $(path1) /hive/data/genomes/mm39/mm39.2bit {check out line+ result/$(file1)} +#ENDLOOP +' > template + + # tac to get some of the smaller ones to run first so it is easy to verify + # it is running OK + ls ../fullChromRun/maf/*.maf | tac > maf.list + + gensub2 maf.list single template jobList + # good to allow plenty of memory, slows them down and allows the large ones + # to finish + para -ram=64g create jobList + para try ... check ... +XXX - running - Sat Dec 19 09:06:14 PST 2020 + para -maxJob=10 push +# Completed: 358 of 358 jobs +# CPU time in finished jobs: 5296s 88.27m 1.47h 0.06d 0.000 y +# IO & Wait Time: 914s 15.23m 0.25h 0.01d 0.000 y +# Average job time: 17s 0.29m 0.00h 0.00d +# Longest finished job: 404s 6.73m 0.11h 0.00d +# Submission to last job: 451s 7.52m 0.13h 0.01d + + du -hsc result + # 156G result + + # Load into database + rm -f /gbdb/mm39/multiz35way/maf/* + cd /hive/data/genomes/mm39/bed/multiz35way/anno/result + + ln -s `pwd`/*.maf /gbdb/mm39/multiz35way/maf/ + + # this generates an immense multiz35way.tab file in the directory + # where it is running. Best to run this over in scratch. + cd /dev/shm + time hgLoadMaf -pathPrefix=/gbdb/mm39/multiz35way/maf mm39 multiz35way + # Loaded 40655883 mafs in 358 files from /gbdb/mm39/multiz35way/maf + # real 37m27.075s + + # -rw-rw-r-- 1 2177747201 Nov 2 18:27 multiz35way.tab + + time (cat /gbdb/mm39/multiz35way/maf/*.maf \ + | hgLoadMafSummary -verbose=2 -minSize=30000 \ + -mergeGap=1500 -maxSize=200000 mm39 multiz35waySummary stdin) +# Created 4568973 summary blocks from 850984320 components and 40655883 mafs from stdin +# real 59m27.383s + +# -rw-rw-r-- 1 2177747201 Nov 2 18:27 multiz35way.tab +# -rw-rw-r-- 1 224894681 Nov 3 08:12 multiz35waySummary.tab + + wc -l multiz35way*.tab + # 40655883 multiz35way.tab + # 4568973 multiz35waySummary.tab + + rm multiz35way*.tab + +############################################################################## +# MULTIZ7WAY MAF FRAMES (TBD - 2017-11-03 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/mm39/bed/multiz35way/frames + cd /hive/data/genomes/mm39/bed/multiz35way/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 == "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 +# mm39: ensGene: 208239, knownGene: 196838, mgcGenes: 35312, ncbiRefSeq: 159322, refGene: 74391, xenoRefGene: 186565, +# panTro5: refGene: 2901, xenoRefGene: 232448, +# panPan2: ncbiRefSeq: 59356, refGene: 130, xenoRefGene: 222742, +# gorGor5: refGene: 444, xenoRefGene: 315030, +# ponAbe2: ensGene: 29447, refGene: 3572, xenoRefGene: 329566, +# nomLeu3: xenoRefGene: 220286, +# rheMac8: ensGene: 56743, refGene: 6481, xenoRefGene: 223255, +# macFas5: refGene: 2164, xenoRefGene: 314695, +# macNem1: refGene: 64, xenoRefGene: 316886, +# cerAty1: refGene: 450, xenoRefGene: 492070, +# papAnu3: ensGene: 31109, refGene: 513, xenoRefGene: 324140, +# chlSab2: ensGene: 28078, xenoRefGene: 245054, +# manLeu1: refGene: 3, xenoRefGene: 456179, +# nasLar1: xenoRefGene: 360558, +# colAng1: ncbiRefSeq: 47349, refGene: 3, xenoRefGene: 332184, +# rhiRox1: xenoRefGene: 364268, +# rhiBie1: xenoRefGene: 342566, +# calJac3: ensGene: 55116, refGene: 228, xenoRefGene: 346395, +# saiBol1: xenoRefGene: 506909, +# cebCap1: refGene: 293, xenoRefGene: 457440, +# aotNan1: refGene: 17, xenoRefGene: 471455, +# tarSyr2: xenoRefGene: 349126, +# micMur3: xenoRefGene: 224817, +# proCoq1: xenoRefGene: 449845, +# eulMac1: xenoRefGene: 427352, +# eulFla1: xenoRefGene: 434365, +# otoGar3: ensGene: 28565, xenoRefGene: 470891, +# mm10: ensGene: 103734, knownGene: 63759, mgcGenes: 27612, ncbiRefSeq: 106520, refGene: 38421, xenoRefGene: 183274, +# canFam3: ensGene: 39074, refGene: 2297, xenoRefGene: 268480, +# dasNov3: ensGene: 37723, xenoRefGene: 500914, + +# real 0m1.505s + + # from that summary, use these gene sets: + # knownGene - mm39 mm10 + # ensGene - ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3 + # xenoRefGene - panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1 + + mkdir genes + + # 1. knownGene: mm39 mm10 + for DB in mm39 mm10 +do + hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from knownGene" ${DB} \ + | genePredSingleCover stdin stdout | gzip -2c \ + > genes/${DB}.gp.gz + genePredCheck -db=${DB} genes/${DB}.gp.gz 2>&1 | sed -e 's/^/ # /;' +done + # checked: 21554 failed: 0 + # checked: 21100 failed: 0 + + # 2. ensGene: ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3 + for DB in ponAbe2 rheMac8 papAnu3 chlSab2 calJac3 otoGar3 canFam3 dasNov3 +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 +# ponAbe2: checked: 20220 failed: 0 +# rheMac8: checked: 20859 failed: 0 +# papAnu3: checked: 19113 failed: 0 +# chlSab2: checked: 19080 failed: 0 +# calJac3: checked: 20827 failed: 0 +# otoGar3: checked: 19472 failed: 0 +# canFam3: checked: 19507 failed: 0 +# dasNov3: checked: 22586 failed: 0 + + # 3. xenoRefGene for panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1 + + for DB in panTro5 panPan2 gorGor5 nomLeu3 macFas5 macNem1 cerAty1 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1 +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 +# panTro5: checked: 21593 failed: 0 +# panPan2: checked: 20031 failed: 0 +# gorGor5: checked: 24721 failed: 0 +# nomLeu3: checked: 20028 failed: 0 +# macFas5: checked: 24291 failed: 0 +# macNem1: checked: 24281 failed: 0 +# cerAty1: checked: 27975 failed: 0 +# manLeu1: checked: 27196 failed: 0 +# nasLar1: checked: 29765 failed: 0 +# colAng1: checked: 24558 failed: 0 +# rhiRox1: checked: 26354 failed: 0 +# rhiBie1: checked: 26930 failed: 0 +# saiBol1: checked: 26867 failed: 0 +# cebCap1: checked: 29673 failed: 0 +# aotNan1: checked: 30988 failed: 0 +# tarSyr2: checked: 29235 failed: 0 +# micMur3: checked: 20083 failed: 0 +# proCoq1: checked: 25577 failed: 0 +# eulMac1: checked: 26918 failed: 0 +# eulFla1: checked: 27223 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/aotNan1.gp.gz: 26592 +# genes/calJac3.gp.gz: 20827 +# genes/canFam3.gp.gz: 19507 +# genes/cebCap1.gp.gz: 25680 +# genes/cerAty1.gp.gz: 24658 +# genes/chlSab2.gp.gz: 19080 +# genes/colAng1.gp.gz: 22290 +# genes/dasNov3.gp.gz: 22586 +# genes/eulFla1.gp.gz: 24120 +# genes/eulMac1.gp.gz: 23994 +# genes/gorGor5.gp.gz: 22552 +# genes/mm39.gp.gz: 21554 +# genes/macFas5.gp.gz: 22206 +# genes/macNem1.gp.gz: 22243 +# genes/manLeu1.gp.gz: 24280 +# genes/micMur3.gp.gz: 19472 +# genes/mm10.gp.gz: 21100 +# genes/nasLar1.gp.gz: 25793 +# genes/nomLeu3.gp.gz: 19509 +# genes/otoGar3.gp.gz: 19472 +# genes/panPan2.gp.gz: 19596 +# genes/panTro5.gp.gz: 20327 +# genes/papAnu3.gp.gz: 19113 +# genes/ponAbe2.gp.gz: 20220 +# genes/proCoq1.gp.gz: 23134 +# genes/rheMac8.gp.gz: 20859 +# genes/rhiBie1.gp.gz: 23979 +# genes/rhiRox1.gp.gz: 23570 +# genes/saiBol1.gp.gz: 23863 +# genes/tarSyr2.gp.gz: 25017 + + + # kluster job to annotate each maf file + screen -S mm39 # manage long running procedure with screen + ssh ku + cd /hive/data/genomes/mm39/bed/multiz35way/frames + + printf '#!/bin/csh -fe + +set C = $1 +set G = $2 + +cat ../maf/${C}.maf | genePredToMafFrames mm39 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).$(root2).mafFrames.gz} +#ENDLOOP +' > template + + mkdir parts + gensub2 chr.list gene.list template jobList + para -ram=64g create jobList + para try ... check ... push +# Completed: 10740 of 10740 jobs +# CPU time in finished jobs: 39407s 656.78m 10.95h 0.46d 0.001 y +# IO & Wait Time: 27424s 457.07m 7.62h 0.32d 0.001 y +# Average job time: 6s 0.10m 0.00h 0.00d +# Longest finished job: 360s 6.00m 0.10h 0.00d +# Submission to last job: 881s 14.68m 0.24h 0.01d + + # collect all results into one file: + cd /hive/data/genomes/mm39/bed/multiz35way/frames + time find ./parts -type f | while read F +do + echo "${F}" 1>&2 + zcat ${F} +done | sort -k1,1 -k2,2n > multiz35wayFrames.bed + # real 2m4.953s + + # -rw-rw-r-- 1 468491708 Nov 3 10:30 multiz35wayFrames.bed + + gzip multiz35wayFrames.bed + + # verify there are frames on everything, should be 46 species: + # (count from: ls genes | wc) + zcat multiz35wayFrames.bed.gz | awk '{print $4}' | sort | uniq -c \ + | sed -e 's/^/# /;' > species.check.list + wc -l species.check.list + # 30 + +# 256062 aotNan1 +# 246852 calJac3 +# 274139 canFam3 +# 251294 cebCap1 +# 258355 cerAty1 +# 214185 chlSab2 +# 244719 colAng1 +# 264484 dasNov3 +# 210815 eulFla1 +# 213386 eulMac1 +# 287686 gorGor5 +# 209184 mm39 +# 253170 macFas5 +# 257891 macNem1 +# 248164 manLeu1 +# 215472 micMur3 +# 260934 mm10 +# 187651 nasLar1 +# 230776 nomLeu3 +# 249009 otoGar3 +# 223118 panPan2 +# 223812 panTro5 +# 193979 papAnu3 +# 200343 ponAbe2 +# 210398 proCoq1 +# 228189 rheMac8 +# 239047 rhiBie1 +# 223257 rhiRox1 +# 248138 saiBol1 +# 222251 tarSyr2 + + # load the resulting file + ssh hgwdev + cd /hive/data/genomes/mm39/bed/multiz35way/frames + time hgLoadMafFrames mm39 multiz35wayFrames multiz35wayFrames.bed.gz + # real 1m13.122s + + hgsql -e 'select count(*) from multiz35wayFrames;' mm39 + # +----------+ + # | count(*) | + # +----------+ + # | 7046760 | + # +----------+ + + time featureBits -countGaps mm39 multiz35wayFrames + # 55160112 bases of 3209286105 (1.719%) in intersection + # real 0m44.816s + + # enable the trackDb entries: +# frames multiz35wayFrames +# irows on + # zoom to base level in an exon to see codon displays + # appears to work OK + +######################################################################### +# Phylogenetic tree from 35-way (TBD - 2013-09-13 - Hiram) + mkdir /hive/data/genomes/mm39/bed/multiz35way/4d + cd /hive/data/genomes/mm39/bed/multiz35way/4d + + # the annotated maf's are in: + ../anno/result/*.maf + + # using knownGene for mm39, 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;" mm39 \ + | 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/mm39/bed/multiz35way/4d/run + cd /hive/data/genomes/mm39/bed/multiz35way/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/mm39/bed/multiz35way" +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/\tmm39.$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/mm39/bed/multiz35way/anno/result/*.maf \ + | sed -e "s#.*multiz35way/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/mm39/bed/multiz35way/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/;//; /^ *$/d' \ + mm39.35way.nh + + sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ + ../mm39.35way.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 +# ((((((((((((mm39:0.0101811,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 ../mm39.35way.nh | grep mm39 \ + | sed -e "s/mm39.//;" | sort > original.dists + + grep TREE all.mod | sed -e 's/TREE: //;' \ + | /cluster/bin/phast/all_dists /dev/stdin | grep mm39 \ + | sed -e "s/mm39.//;" | sort > mm39.dists + + # printing out the 'original', the 'new' the 'difference' and + # percent difference/delta + join original.dists mm39.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 35-way (TBD - 2015-05-07 - Hiram) + # split 35way mafs into 10M chunks and generate sufficient statistics + # files for # phastCons + ssh ku + mkdir -p /hive/data/genomes/mm39/bed/multiz35way/cons/ss + mkdir -p /hive/data/genomes/mm39/bed/multiz35way/cons/msa.split + cd /hive/data/genomes/mm39/bed/multiz35way/cons/msa.split + + cat << '_EOF_' > doSplit.csh +#!/bin/csh -ef +set c = $1 +set MAF = /hive/data/genomes/mm39/bed/multiz35way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/mm39/bed/multiz35way/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 = $1 +set MAF = /hive/data/genomes/mm39/bed/multiz35way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/mm39/bed/multiz35way/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/mm39/bed/multiz35way/cons/run.cons + cd /hive/data/genomes/mm39/bed/multiz35way/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/mm39/bed/multiz35way/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/mm39/bed/multiz35way/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/mm39/bed/multiz35way/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/mm39/bed/multiz35way/cons/all + time hgLoadBed mm39 phastConsElements35way 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 mm39 -enrichment knownGene:cds phastConsElements35way +# knownGene:cds 1.271%, phastConsElements35way 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 mm39 -enrichment refGene:cds phastConsElements35way +# refGene:cds 1.225%, phastConsElements35way 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/mm39/bed/multiz35way/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}.phastCons35way.wigFix.gz +done + # real 32m29.089s + + + # encode those files into wiggle data + time (zcat downloads/*.wigFix.gz \ + | wigEncode stdin phastCons35way.wig phastCons35way.wib) + # Converted stdin, upper limit 1.00, lower limit 0.00 + # real 15m40.010s + + du -hsc *.wi? + # 2.8G phastCons35way.wib + # 283M phastCons35way.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 phastCons35way.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 phastCons35way.bw + + + bigWigInfo phastCons35way.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/mm39/bbi + ln -s `pwd`/phastCons35way.bw /gbdb/mm39/bbi + hgsql mm39 -e 'drop table if exists phastCons35way; \ + create table phastCons35way (fileName varchar(255) not null); \ + insert into phastCons35way values + ("/gbdb/mm39/bbi/phastCons35way.bw");' + + # Load gbdb and database with wiggle. + ssh hgwdev + cd /hive/data/genomes/mm39/bed/multiz35way/cons/all + ln -s `pwd`/phastCons35way.wib /gbdb/mm39/multiz35way/phastCons35way.wib + time hgLoadWiggle -pathPrefix=/gbdb/mm39/multiz35way mm39 \ + phastCons35way phastCons35way.wig + # real 0m32.272s + + time wigTableStats.sh mm39 phastCons35way +# db.table min max mean count sumData +# mm39.phastCons35way 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/mm39/bed/multiz35way/cons/all + time hgWiggle -doHistogram -db=mm39 \ + -hBinSize=0.001 -hBinCount=300 -hMinVal=0.0 -verbose=2 \ + phastCons35way > 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 Mm39 Histogram phastCons35way track" +set xlabel " phastCons35way 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 35-way (TBD - 2017-11-06 - Hiram) +# + # split SS files into 1M chunks, this business needs smaller files + # to complete + + ssh ku + mkdir /hive/data/genomes/mm39/bed/multiz35way/consPhyloP + cd /hive/data/genomes/mm39/bed/multiz35way/consPhyloP + mkdir ss run.split + cd run.split + + printf '#!/bin/csh -ef +set c = $1 +set MAF = /hive/data/genomes/mm39/bed/multiz35way/anno/result/$c.maf +set WINDOWS = /hive/data/genomes/mm39/bed/multiz35way/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/mm39/bed/multiz35way/consPhyloP + cd /cluster/data/mm39/bed/multiz35way/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/mm39/bed/multiz35way/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/mm39/bed/multiz35way/consPhyloP/all + cd /hive/data/genomes/mm39/bed/multiz35way/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}.phyloP35way.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/mm39/chrom.sizes \ + phyloP35way.bw) > bigWig.log 2>&1 + + + egrep "real|VmPeak" bigWig.log + # pid=66292: VmPeak: 33751268 kB + # real 43m40.194s + + + bigWigInfo phyloP35way.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 phyloP35way.wig phyloP35way.wib) + +# Converted stdin, upper limit 1.31, lower limit -20.00 +# real 17m36.880s +# -rw-rw-r-- 1 2955660581 Nov 6 14:10 phyloP35way.wib +# -rw-rw-r-- 1 304274846 Nov 6 14:10 phyloP35way.wig + + du -hsc *.wi? + # 2.8G phyloP35way.wib + # 291M phyloP35way.wig + + # Load gbdb and database with wiggle. + ln -s `pwd`/phyloP35way.wib /gbdb/mm39/multiz35way/phyloP35way.wib + time hgLoadWiggle -pathPrefix=/gbdb/mm39/multiz35way mm39 \ + phyloP35way phyloP35way.wig + # real 0m30.538s + + # use to set trackDb.ra entries for wiggle min and max + # and verify table is loaded correctly + + wigTableStats.sh mm39 phyloP35way +# db.table min max mean count sumData +# mm39.phyloP35way -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=mm39 phyloP35way > 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 mm39 Histogram phyloP35way track" +set xlabel " phyloP35way 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 35-way (TBD - 2015-04-15 - Hiram) + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/multiz35way + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phastCons35way + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phyloP35way + mkdir /hive/data/genomes/mm39/bed/multiz35way/downloads + cd /hive/data/genomes/mm39/bed/multiz35way/downloads + mkdir multiz35way phastCons35way phyloP35way + + ######################################################################### + ## create upstream refGene maf files + cd /hive/data/genomes/mm39/bed/multiz35way/downloads/multiz35way + # bash script + +#!/bin/sh +export geneTbl="refGene" +for S in 300 2000 5000 +do + echo "making upstream${S}.maf" + featureBits mm39 ${geneTbl}:upstream:${S} -fa=/dev/null -bed=stdout \ + | perl -wpe 's/_up[^\t]+/\t0/' | sort -k1,1 -k2,2n \ + | /cluster/bin/$MACHTYPE/mafFrags mm39 multiz35way \ + stdin stdout \ + -orgs=/hive/data/genomes/mm39/bed/multiz35way/species.list \ + | gzip -c > upstream${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/mm39/bed/multiz35way/downloads/multiz35way + 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/mm39/multiz35way/maf + cd maf + ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/multiz35way/maf + cd -- + ln -s `pwd`/*.maf.gz `pwd`/*.nh `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/multiz35way/ + + ########################################################################### + + cd /hive/data/genomes/mm39/bed/multiz35way/downloads/multiz35way + grep TREE ../../4d/all.mod | awk '{print $NF}' \ + | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > mm39.35way.nh + ~/kent/src/hg/utils/phyloTrees/commonNames.sh mm39.35way.nh \ + | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > mm39.35way.commonNames.nh + ~/kent/src/hg/utils/phyloTrees/scientificNames.sh mm39.35way.nh \ + | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ + > mm39.35way.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/mm39/multiz35way + + du -hsc ./maf ../../anno/result + # 18G ./maf + # 156G ../../anno/result + + # obtain the README.txt from mm39/multiz20way and update for this + # situation + ln -s `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/multiz35way/ + + ##################################################################### + cd /hive/data/genomes/mm39/bed/multiz35way/downloads/phastCons35way + + mkdir mm39.35way.phastCons + cd mm39.35way.phastCons + ln -s ../../../cons/all/downloads/*.wigFix.gz . + md5sum *.gz > md5sum.txt + + cd /hive/data/genomes/mm39/bed/multiz35way/downloads/phastCons35way + ln -s ../../cons/all/phastCons35way.bw ./mm39.phastCons35way.bw + ln -s ../../cons/all/all.mod ./mm39.phastCons35way.mod + time md5sum *.mod *.bw > md5sum.txt + # real 0m20.354s + + # obtain the README.txt from mm39/phastCons20way and update for this + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phastCons35way/mm39.35way.phastCons + cd mm39.35way.phastCons + ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phastCons35way/mm39.35way.phastCons + + cd .. + # situation + ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phastCons35way + + ##################################################################### + cd /hive/data/genomes/mm39/bed/multiz35way/downloads/phyloP35way + + mkdir mm39.35way.phyloP + cd mm39.35way.phyloP + + ln -s ../../../consPhyloP/all/downloads/*.wigFix.gz . + md5sum *.wigFix.gz > md5sum.txt + + cd .. + + ln -s ../../consPhyloP/run.phyloP/all.mod mm39.phyloP35way.mod + ln -s ../../consPhyloP/all/phyloP35way.bw mm39.phyloP35way.bw + + md5sum *.mod *.bw > md5sum.txt + + # obtain the README.txt from mm39/phyloP20way and update for this + mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phyloP35way/mm39.35way.phyloP + cd mm39.35way.phyloP + ln -s `pwd`/* \ +/usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phyloP35way/mm39.35way.phyloP + + cd .. + + # situation + ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ + /usr/local/apache/htdocs-hgdownload/goldenPath/mm39/phyloP35way + +############################################################################# +# hgPal downloads (TBD - 2017-11-06 - Hiram) +# FASTA from 35-way for knownGene, refGene and knownCanonical + + ssh hgwdev + screen -S mm39HgPal + mkdir /hive/data/genomes/mm39/bed/multiz35way/pal + cd /hive/data/genomes/mm39/bed/multiz35way/pal + cat ../species.list | tr '[ ]' '[\n]' > order.list + + ### knownCanonical with full CDS + cd /hive/data/genomes/mm39/bed/multiz35way/pal + export mz=multiz35way + export gp=knownCanonical + export db=mm39 + mkdir exonAA exonNuc knownCanonical + + time cut -f1 ../../../chrom.sizes | while read C + do + echo $C 1>&2 + hgsql mm39 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$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=multiz35way + export gp=knownCanonical + export db=mm39 + 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/mm39/bed/multiz100way/pal + export mz=multiz100way + export gp=knownCanonical + export db=mm39 + mkdir exonAA exonNuc knownCanonical + + time cut -f1 ../../../chrom.sizes | while read C + do + echo $C 1>&2 + hgsql mm39 -N -e "select chrom, chromStart, chromEnd, transcript from knownCanonical where chrom='$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=multiz35way + export gp=knownCanonical + export db=mm39 + 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=mm39 + 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 $pd + md5sum *.fa.gz > md5sum.txt + + rm -rf exonAA exonNuc + + export mz=multiz35way + export gp=knownCanonical + export db=mm39 + export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$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=multiz35way + export gp=knownGene + export db=mm39 + 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=multiz35way + 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.multiz35way.exonAA.fa.gz + # -rw-rw-r-- 1 580377720 Nov 6 18:49 knownGene.multiz35way.exonNuc.fa.gz + + export mz=multiz35way + export gp=knownGene + export db=mm39 + 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 35-way (TBD - 2017-11-06 - Hiram) + mkdir /hive/users/hiram/bigWays/mm39.35way + cd /hive/users/hiram/bigWays + echo "mm39" > mm39.35way/ordered.list + awk '{print $1}' /hive/data/genomes/mm39/bed/multiz35way/35way.distances.txt \ + >> mm39.35way/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 mm39.35way/ordered.list + # dbDb.sh constructs mm39.35way/XenTro9_35-way_conservation_alignment.html + # may need to add new assembly references to srcReference.list and + # urlReference.list + ./dbDb.sh mm39 35way + # sizeStats.pl constructs mm39.35way/XenTro9_35-way_Genome_size_statistics.html + # this requires entries in coverage.list for new sequences + ./sizeStats.pl mm39 35way + + # defCheck.pl constructs XenTro9_35-way_conservation_lastz_parameters.html + ./defCheck.pl mm39 35way + + # this constructs the html pages in mm39.35way/: +# -rw-rw-r-- 1 6247 May 2 17:07 XenTro9_35-way_conservation_alignment.html +# -rw-rw-r-- 1 8430 May 2 17:09 XenTro9_35-way_Genome_size_statistics.html +# -rw-rw-r-- 1 5033 May 2 17:10 XenTro9_35-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_35-way_conservation_alignment +# XenTro9_35-way_Genome_size_statistics +# XenTro9_35-way_conservation_lastz_parameters + + # when you view the first one you enter, it will have links to the + # missing two. + +############################################################################ +# pushQ readmine (TBD - 2017-11-07 - Hiram) + + cd /usr/local/apache/htdocs-hgdownload/goldenPath/mm39 + find -L `pwd`/multiz35way `pwd`/phastCons35way `pwd`/phyloP35way \ + /gbdb/mm39/multiz35way -type f \ + > /hive/data/genomes/mm39/bed/multiz35way/downloads/redmine.20216.fileList + wc -l /hive/data/genomes/mm39/bed/multiz35way/downloads/redmine.20216.fileList +# 1450 /hive/data/genomes/mm39/bed/multiz35way/downloads/redmine.20216.fileList + + cd /hive/data/genomes/mm39/bed/multiz35way/downloads + hgsql -e 'show tables;' mm39 | grep 35way \ + | sed -e 's/^/mm39./;' > redmine.20216.table.list + +############################################################################