8b84f22d1b235ac3dcc37d35e2c051d3e6e36292 braney Wed Nov 6 14:08:46 2019 -0800 generate new CDS FASTA files for multiz30way diff --git src/hg/makeDb/doc/hg38/multiz30way.txt src/hg/makeDb/doc/hg38/multiz30way.txt index fce4b35..fba1544 100644 --- src/hg/makeDb/doc/hg38/multiz30way.txt +++ src/hg/makeDb/doc/hg38/multiz30way.txt @@ -1,1983 +1,2085 @@ ############################################################################# ## 30-Way Multiz (DONE - 2017-10-19 - Hiram) ssh hgwdev mkdir /hive/data/genomes/hg38/bed/multiz30way cd /hive/data/genomes/hg38/bed/multiz30way # from the 218-way in the source tree, select out the 30 used here: /cluster/bin/phast/tree_doctor \ --prune-all-but aotNan1,calJac3,cebCap1,cerAty1,chlSab2,colAng1,eulFla1,eulMac1,gorGor5,hg38,macFas5,macNem1,manLeu1,micMur3,nasLar1,nomLeu3,otoGar3,panPan2,panTro5,papAnu3,ponAbe2,proCoq1,rheMac8,rhiBie1,rhiRox1,saiBol1,tarSyr2,canFam3,dasNov3,mm10 \ /cluster/home/hiram/kent/src/hg/utils/phyloTrees/218way.nh \ > 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/;' # panTro5 0.013390 # panPan2 0.015610 # gorGor5 0.019734 # ponAbe2 0.039403 # nomLeu3 0.046204 # nasLar1 0.075474 # rhiBie1 0.075474 # rhiRox1 0.075474 # colAng1 0.075574 # macFas5 0.079575 # rheMac8 0.079575 # papAnu3 0.079626 # macNem1 0.081584 # cerAty1 0.082584 # saiBol1 0.087804 # chlSab2 0.087974 # manLeu1 0.090974 # aotNan1 0.102804 # calJac3 0.107454 # cebCap1 0.108804 # eulFla1 0.190934 # eulMac1 0.190934 # tarSyr2 0.221294 # proCoq1 0.230934 # micMur3 0.236534 # otoGar3 0.270334 # canFam3 0.332429 # dasNov3 0.366691 # mm10 0.502391 # what that looks like: ~/kent/src/hg/utils/phyloTrees/asciiTree.pl t.nh > hg38.30way.nh ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.30way.nh | sed -e 's/^/# /;' # ((((((((((((hg38:0.00655, # panTro5:0.00684):0.00122, # panPan2:0.00784):0.003, # gorGor5:0.008964):0.009693, # ponAbe2:0.01894):0.003471, # nomLeu3:0.02227):0.01204, # (((((rheMac8:0.003991, # (macFas5:0.002991, # macNem1:0.005000):0.001000):0.001000, # cerAty1:0.008):0.005, # papAnu3:0.010042):0.01061, # (chlSab2:0.027, # manLeu1:0.030000):0.002000):0.003000, # ((nasLar1:0.0007, # colAng1:0.0008):0.0008, # (rhiRox1:0.0007, # rhiBie1:0.000700):0.000800):0.018000):0.020000):0.021830, # (((calJac3:0.03, # saiBol1:0.01035):0.00865, # cebCap1:0.04):0.006, # aotNan1:0.040000):0.005000):0.052090, # tarSyr2:0.1114):0.02052, # (((micMur3:0.0556, # proCoq1:0.05):0.015, # (eulMac1:0.01, # eulFla1:0.010000):0.015000):0.015000, # otoGar3:0.119400):0.020520):0.015494, # mm10:0.356483):0.020593, # canFam3:0.165928):0.023664, # dasNov3:0.176526); # extract species list from that .nh file sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ hg38.30way.nh | xargs echo | sed 's/ //g; s/,/ /g' \ | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt # construct db to name translation list: cat species.list.txt | while read DB do hgsql -N -e "select name,organism from dbDb where name=\"${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`" hg38.30way.nh \ | sed -e 's/0\+)/)/g; s/0\+,/,/g' \ | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ | sed -e "s#_x_#'#g;" > hg38.30way.commonNames.nh cat hg38.30way.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/hg38_30way.png ~/kent/src/hg/utils/phyloTrees/asciiTree.pl hg38.30way.nh > t.nh ~/kent/src/hg/utils/phyloTrees/scientificNames.sh t.nh \ | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ > hg38.30way.scientificNames.nh rm -f t.nh cat hg38.30way.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 hg38.30way.nh | grep hg38 \ | sed -e "s/hg38.//" | sort -k2n > 30way.distances.txt # Use this output to create the table below cat 30way.distances.txt | sed -e 's/^/# /;' # panTro5 0.013390 # panPan2 0.015610 # gorGor5 0.019734 # ponAbe2 0.039403 # nomLeu3 0.046204 # nasLar1 0.075474 # rhiBie1 0.075474 # rhiRox1 0.075474 # colAng1 0.075574 # macFas5 0.079575 # rheMac8 0.079575 # papAnu3 0.079626 # macNem1 0.081584 # cerAty1 0.082584 # saiBol1 0.087804 # chlSab2 0.087974 # manLeu1 0.090974 # aotNan1 0.102804 # calJac3 0.107454 # cebCap1 0.108804 # eulFla1 0.190934 # eulMac1 0.190934 # tarSyr2 0.221294 # proCoq1 0.230934 # micMur3 0.236534 # otoGar3 0.270334 # canFam3 0.332429 # dasNov3 0.366691 # mm10 0.502391 printf '#!/usr/bin/env perl use strict; use warnings; open (FH, "<30way.distances.txt") or die "can not read 30way.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 (% 95.355) (% 93.714) - Chimp panTro5 # 02 0.0156 (% 92.685) (% 97.742) - Bonobo panPan2 # 03 0.0197 (% 94.691) (% 89.804) - Gorilla gorGor5 # 04 0.0394 (% 89.187) (% 89.656) - Orangutan ponAbe2 # 05 0.0462 (% 86.379) (% 90.470) - Gibbon nomLeu3 # 06 0.0755 (% 74.541) (% 89.972) - Proboscis monkey nasLar1 # 07 0.0755 (% 83.065) (% 81.306) - Black snub-nosed monkey rhiBie1 # 08 0.0755 (% 85.109) (% 86.629) - Golden snub-nosed monkey rhiRox1 # 09 0.0756 (% 81.641) (% 87.875) - Angolan colobus colAng1 # 10 0.0796 (% 85.675) (% 87.749) - Crab-eating macaque macFas5 # 11 0.0796 (% 84.506) (% 79.540) - Rhesus rheMac8 # 12 0.0796 (% 86.336) (% 86.461) - Baboon papAnu3 # 13 0.0816 (% 83.524) (% 85.402) - Pig-tailed macaque macNem1 # 14 0.0826 (% 83.847) (% 86.974) - Sooty mangabey cerAty1 # 15 0.0878 (% 70.565) (% 81.466) - Squirrel monkey saiBol1 # 16 0.0880 (% 84.393) (% 88.264) - Green monkey chlSab2 # 17 0.0910 (% 82.498) (% 88.550) - Drill manLeu1 # 18 0.1028 (% 70.629) (% 77.791) - Ma's night monkey aotNan1 # 19 0.1075 (% 71.709) (% 76.757) - Marmoset calJac3 # 20 0.1088 (% 70.683) (% 78.656) - White-faced sapajou cebCap1 # 21 0.1909 (% 33.326) (% 46.309) - Sclater's lemur eulFla1 # 22 0.1909 (% 33.708) (% 46.640) - Black lemur eulMac1 # 23 0.2213 (% 56.022) (% 52.305) - Tarsier tarSyr2 # 24 0.2309 (% 32.467) (% 45.739) - Coquerel's sifaka proCoq1 # 25 0.2365 (% 29.728) (% 36.904) - Mouse lemur micMur3 # 26 0.2703 (% 53.196) (% 64.899) - Bushbaby otoGar3 # 27 0.3324 (% 50.395) (% 60.861) - Dog canFam3 # 28 0.3667 (% 45.349) (% 41.895) - Armadillo dasNov3 # 29 0.5024 (% 31.653) (% 35.372) - Mouse mm10 # 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' \ hg38.30way.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 panTro5 panPan2 gorGor5 ponAbe2 nomLeu3 rheMac8 macFas5 macNem1 # cerAty1 papAnu3 chlSab2 manLeu1 nasLar1 colAng1 rhiRox1 rhiBie1 calJac3 # saiBol1 cebCap1 aotNan1 tarSyr2 micMur3 proCoq1 eulMac1 eulFla1 otoGar3 # mm10 canFam3 dasNov3 # bash shell syntax here ... cd /hive/data/genomes/hg38/bed/multiz30way export H=/hive/data/genomes/hg38/bed mkdir mafLinks # good, phylo close assemblies can use syntenic net: for G in panTro5 panPan2 gorGor5 nomLeu3 colAng1 macFas5 rheMac8 macNem1 \ cerAty1 saiBol1 chlSab2 manLeu1 aotNan1 calJac3 cebCap1 proCoq1 micMur3 \ otoGar3 canFam3 dasNov3 mm10 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 # other assemblies using recip best net: # for G in ponAbe2 nasLar1 rhiBie1 rhiRox1 papAnu3 eulFla1 eulMac1 tarSyr2 do mkdir mafLinks/$G echo ln -s ${H}/lastz.$G/mafRBestNet/hg38.${G}.rbest.maf.gz ./mafLinks/$G ln -s ${H}/lastz.$G/mafRBestNet/hg38.${G}.rbest.maf.gz ./mafLinks/$G done # verify the symLinks are good: ls -ogL mafLinks/*/* | sed -e 's/^/# /; s/-rw-rw-r-- 1//;' # 1234251218 Sep 25 17:10 mafLinks/aotNan1/hg38.aotNan1.synNet.maf.gz # 1275300135 Dec 13 2014 mafLinks/calJac3/hg38.calJac3.synNet.maf.gz # 1098577678 Apr 10 2015 mafLinks/canFam3/hg38.canFam3.synNet.maf.gz # 1254406823 Sep 28 20:27 mafLinks/cebCap1/hg38.cebCap1.synNet.maf.gz # 1364636284 Sep 27 12:27 mafLinks/cerAty1/hg38.cerAty1.synNet.maf.gz # 1375738965 Jul 11 2014 mafLinks/chlSab2/hg38.chlSab2.synNet.maf.gz # 1317115105 Feb 27 2017 mafLinks/colAng1/hg38.colAng1.synNet.maf.gz # 973195648 Apr 29 2015 mafLinks/dasNov3/hg38.dasNov3.synNet.maf.gz # 669135484 Oct 5 14:41 mafLinks/eulFla1/hg38.eulFla1.rbest.maf.gz # 677123602 Oct 5 13:04 mafLinks/eulMac1/hg38.eulMac1.rbest.maf.gz # 1649008320 Jun 25 2016 mafLinks/gorGor5/hg38.gorGor5.synNet.maf.gz # 1403994424 Dec 14 2014 mafLinks/macFas5/hg38.macFas5.synNet.maf.gz # 1356256046 Feb 27 2017 mafLinks/macNem1/hg38.macNem1.synNet.maf.gz # 1334057905 Sep 25 10:05 mafLinks/manLeu1/hg38.manLeu1.synNet.maf.gz # 611966540 Mar 4 2017 mafLinks/micMur3/hg38.micMur3.synNet.maf.gz # 710111073 Apr 9 2015 mafLinks/mm10/hg38.mm10.synNet.maf.gz # 1145326563 Dec 15 2014 mafLinks/nasLar1/hg38.nasLar1.rbest.maf.gz # 1333531476 Dec 12 2014 mafLinks/nomLeu3/hg38.nomLeu3.synNet.maf.gz # 1130201295 Feb 23 2015 mafLinks/otoGar3/hg38.otoGar3.synNet.maf.gz # 1514679150 May 24 2016 mafLinks/panPan2/hg38.panPan2.synNet.maf.gz # 1642086478 Aug 4 2016 mafLinks/panTro5/hg38.panTro5.synNet.maf.gz # 1336353318 Jun 22 23:34 mafLinks/papAnu3/hg38.papAnu3.rbest.maf.gz # 1274517712 Sep 3 2014 mafLinks/ponAbe2/hg38.ponAbe2.rbest.maf.gz # 652745807 Sep 28 19:12 mafLinks/proCoq1/hg38.proCoq1.synNet.maf.gz # 1369672577 Feb 8 2016 mafLinks/rheMac8/hg38.rheMac8.synNet.maf.gz # 1268717561 Mar 29 2017 mafLinks/rhiBie1/hg38.rhiBie1.rbest.maf.gz # 1312210382 Feb 24 2015 mafLinks/rhiRox1/hg38.rhiRox1.rbest.maf.gz # 1257517046 Dec 13 2014 mafLinks/saiBol1/hg38.saiBol1.synNet.maf.gz # 1109719031 Dec 13 2014 mafLinks/tarSyr2/hg38.tarSyr2.rbest.maf.gz # need to split these things up into smaller pieces for # efficient kluster run. mkdir /hive/data/genomes/hg38/bed/multiz30way/mafSplit cd /hive/data/genomes/hg38/bed/multiz30way/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 hg38 5 stdout | sort -u \ | sort -k1,1 -k2,2n > mafSplit.bed # see also multiz30way.txt for more discussion of this procedure # run a kluster job to split them all ssh ku cd /hive/data/genomes/hg38/bed/multiz30way/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,$4}' \ | sed -e 's/.maf.gz//;' > maf.list gensub2 maf.list single template jobList para -ram=16g create jobList para try ... check ... push ... etc... # Completed: 29 of 29 jobs # CPU time in finished jobs: 31855s 530.92m 8.85h 0.37d 0.001 y # IO & Wait Time: 0s 0.00m 0.00h 0.00d 0.000 y # Average job time: 1070s 17.84m 0.30h 0.01d # Longest finished job: 1544s 25.73m 0.43h 0.02d # Submission to last job: 3302s 55.03m 0.92h 0.04d # construct a list of all possible maf file names. # they do not all exist in each of the species directories find . -type f | grep "maf.gz" | wc -l # 16567 find . -type f | grep ".maf.gz$" | 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/hg38_//;' \ | sort | uniq -c | sort -n | wc -l # 358 mkdir /hive/data/genomes/hg38/bed/multiz30way/splitRun cd /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way/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 $(root1) {check out line+ /hive/data/genomes/hg38/bed/multiz30way/splitRun/maf/$(root1)} #ENDLOOP ' > template ln -s ../../mafSplit/run.maf.list maf.list ssh ku cd /hive/data/genomes/hg38/bed/multiz30way/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/hg38/bed/multiz30way/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/${C}.maf.gz endif if ( -s maf/hg38_${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 '_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/hg38/bed/multiz30way/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/hg38/bed/multiz30way/maf # 97 of them have empty results, they have to be removed ls -ogrt | awk '$3 == 0' | awk '{print $NF}' | xargs rm -f # Load into database mkdir -p /gbdb/hg38/multiz30way/maf cd /hive/data/genomes/hg38/bed/multiz30way/maf ln -s `pwd`/*.maf /gbdb/hg38/multiz30way/maf/ # this generates an immense multiz30way.tab file in the directory # where it is running. Best to run this over in scratch. # This is going to take all day. cd /dev/shm time hgLoadMaf -pathPrefix=/gbdb/hg38/multiz30way/maf hg38 multiz30way # Loaded 40625470 mafs in 358 files from /gbdb/hg38/multiz30way/maf # real 28m23.045s time (cat /gbdb/hg38/multiz30way/maf/*.maf \ | hgLoadMafSummary -verbose=2 -minSize=30000 \ -mergeGap=1500 -maxSize=200000 hg38 multiz30waySummary stdin) # Created 4568973 summary blocks from 850984320 components and 40625470 mafs from stdin # real 49m52.561s -rw-rw-r-- 1 2171190193 Nov 2 16:40 multiz30way.tab -rw-rw-r-- 1 215756735 Nov 2 17:44 multiz30waySummary.tab wc -l multiz30*.tab # 40625470 multiz30way.tab # 4568973 multiz30waySummary.tab rm multiz30way*.tab ####################################################################### # GAP ANNOTATE MULTIZ30WAY MAF AND LOAD TABLES (DONE - 2017-11-03 - Hiram) # mafAddIRows has to be run on single chromosome maf files, it does not # function correctly when more than one reference sequence # are in a single file. mkdir -p /hive/data/genomes/hg38/bed/multiz30way/anno cd /hive/data/genomes/hg38/bed/multiz30way/anno # check for N.bed files everywhere: for DB in `cat ../species.list` do if [ ! -s /hive/data/genomes/${DB}/${DB}.N.bed ]; then echo "MISS: ${DB}" cd /hive/data/genomes/${DB} twoBitInfo -nBed ${DB}.2bit ${DB}.N.bed else echo " OK: ${DB}" fi cd /hive/data/genomes/hg38/bed/multiz30way/anno done cd /hive/data/genomes/hg38/bed/multiz30way/anno for DB in `cat ../species.list` do echo "${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/multiz30way/anno mkdir result cat << '_EOF_' > template #LOOP mafAddIRows -nBeds=nBeds $(path1) /hive/data/genomes/hg38/hg38.2bit {check out line+ result/$(file1)} #ENDLOOP '_EOF_' # << 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: 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/hg38/multiz30way/maf/* cd /hive/data/genomes/hg38/bed/multiz30way/anno/result ln -s `pwd`/*.maf /gbdb/hg38/multiz30way/maf/ # this generates an immense multiz30way.tab file in the directory # where it is running. Best to run this over in scratch. cd /dev/shm time hgLoadMaf -pathPrefix=/gbdb/hg38/multiz30way/maf hg38 multiz30way # Loaded 40655883 mafs in 358 files from /gbdb/hg38/multiz30way/maf # real 37m27.075s # -rw-rw-r-- 1 2177747201 Nov 2 18:27 multiz30way.tab time (cat /gbdb/hg38/multiz30way/maf/*.maf \ | hgLoadMafSummary -verbose=2 -minSize=30000 \ -mergeGap=1500 -maxSize=200000 hg38 multiz30waySummary 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 multiz30way.tab # -rw-rw-r-- 1 224894681 Nov 3 08:12 multiz30waySummary.tab wc -l multiz30way*.tab # 40655883 multiz30way.tab # 4568973 multiz30waySummary.tab rm multiz30way*.tab ############################################################################## # MULTIZ7WAY MAF FRAMES (DONE - 2017-11-03 - Hiram) ssh hgwdev mkdir /hive/data/genomes/hg38/bed/multiz30way/frames cd /hive/data/genomes/hg38/bed/multiz30way/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 # hg38: 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 - hg38 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: hg38 mm10 for DB in hg38 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/hg38.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 hg38 # manage long running procedure with screen ssh ku cd /hive/data/genomes/hg38/bed/multiz30way/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).$(root2).mafFrames.gz} #ENDLOOP ' > template mkdir parts gensub2 chr.list gene.list template jobList para -ram=64g create jobList para try ... check ... push # Completed: 10740 of 10740 jobs # CPU time in finished jobs: 39407s 656.78m 10.95h 0.46d 0.001 y # IO & Wait Time: 27424s 457.07m 7.62h 0.32d 0.001 y # Average job time: 6s 0.10m 0.00h 0.00d # Longest finished job: 360s 6.00m 0.10h 0.00d # Submission to last job: 881s 14.68m 0.24h 0.01d # collect all results into one file: cd /hive/data/genomes/hg38/bed/multiz30way/frames time find ./parts -type f | while read F do echo "${F}" 1>&2 zcat ${F} done | sort -k1,1 -k2,2n > multiz30wayFrames.bed # real 2m4.953s # -rw-rw-r-- 1 468491708 Nov 3 10:30 multiz30wayFrames.bed gzip multiz30wayFrames.bed # verify there are frames on everything, should be 46 species: # (count from: ls genes | wc) zcat multiz30wayFrames.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 hg38 # 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/hg38/bed/multiz30way/frames time hgLoadMafFrames hg38 multiz30wayFrames multiz30wayFrames.bed.gz # real 1m13.122s hgsql -e 'select count(*) from multiz30wayFrames;' hg38 # +----------+ # | count(*) | # +----------+ # | 7046760 | # +----------+ time featureBits -countGaps hg38 multiz30wayFrames # 55160112 bases of 3209286105 (1.719%) in intersection # real 0m44.816s # enable the trackDb entries: # frames multiz30wayFrames # irows on # zoom to base level in an exon to see codon displays # appears to work OK ######################################################################### # Phylogenetic tree from 30-way (DONE - 2013-09-13 - Hiram) mkdir /hive/data/genomes/hg38/bed/multiz30way/4d cd /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way/4d/run cd /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way" 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/multiz30way/anno/result/*.maf \ | sed -e "s#.*multiz30way/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/multiz30way/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/;//; /^ *$/d' \ hg38.30way.nh sed 's/[a-z][a-z]*_//g; s/:[0-9\.][0-9\.]*//g; s/;//; /^ *$/d' \ ../hg38.30way.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 ../hg38.30way.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 30way mafs into 10M chunks and generate sufficient statistics # files for # phastCons ssh ku mkdir -p /hive/data/genomes/hg38/bed/multiz30way/cons/ss mkdir -p /hive/data/genomes/hg38/bed/multiz30way/cons/msa.split cd /hive/data/genomes/hg38/bed/multiz30way/cons/msa.split cat << '_EOF_' > doSplit.csh #!/bin/csh -ef set c = $1 set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/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 = $1 set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way/cons/run.cons cd /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way/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/multiz30way/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/multiz30way/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/multiz30way/cons/all time hgLoadBed hg38 phastConsElements30way 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 phastConsElements30way # knownGene:cds 1.271%, phastConsElements30way 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 phastConsElements30way # refGene:cds 1.225%, phastConsElements30way 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/multiz30way/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}.phastCons30way.wigFix.gz done # real 32m29.089s # encode those files into wiggle data time (zcat downloads/*.wigFix.gz \ | wigEncode stdin phastCons30way.wig phastCons30way.wib) # Converted stdin, upper limit 1.00, lower limit 0.00 # real 15m40.010s du -hsc *.wi? # 2.8G phastCons30way.wib # 283M phastCons30way.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 phastCons30way.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 phastCons30way.bw bigWigInfo phastCons30way.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`/phastCons30way.bw /gbdb/hg38/bbi hgsql hg38 -e 'drop table if exists phastCons30way; \ create table phastCons30way (fileName varchar(255) not null); \ insert into phastCons30way values ("/gbdb/hg38/bbi/phastCons30way.bw");' # Load gbdb and database with wiggle. ssh hgwdev cd /hive/data/genomes/hg38/bed/multiz30way/cons/all ln -s `pwd`/phastCons30way.wib /gbdb/hg38/multiz30way/phastCons30way.wib time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz30way hg38 \ phastCons30way phastCons30way.wig # real 0m32.272s time wigTableStats.sh hg38 phastCons30way # db.table min max mean count sumData # hg38.phastCons30way 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/multiz30way/cons/all time hgWiggle -doHistogram -db=hg38 \ -hBinSize=0.001 -hBinCount=300 -hMinVal=0.0 -verbose=2 \ phastCons30way > 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 phastCons30way track" set xlabel " phastCons30way 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/multiz30way/consPhyloP cd /hive/data/genomes/hg38/bed/multiz30way/consPhyloP mkdir ss run.split cd run.split printf '#!/bin/csh -ef set c = $1 set MAF = /hive/data/genomes/hg38/bed/multiz30way/anno/result/$c.maf set WINDOWS = /hive/data/genomes/hg38/bed/multiz30way/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/multiz30way/consPhyloP cd /cluster/data/hg38/bed/multiz30way/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/multiz30way/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/multiz30way/consPhyloP/all cd /hive/data/genomes/hg38/bed/multiz30way/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}.phyloP30way.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 \ phyloP30way.bw) > bigWig.log 2>&1 egrep "real|VmPeak" bigWig.log # pid=66292: VmPeak: 33751268 kB # real 43m40.194s bigWigInfo phyloP30way.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 phyloP30way.wig phyloP30way.wib) # Converted stdin, upper limit 1.31, lower limit -20.00 # real 17m36.880s # -rw-rw-r-- 1 2955660581 Nov 6 14:10 phyloP30way.wib # -rw-rw-r-- 1 304274846 Nov 6 14:10 phyloP30way.wig du -hsc *.wi? # 2.8G phyloP30way.wib # 291M phyloP30way.wig # Load gbdb and database with wiggle. ln -s `pwd`/phyloP30way.wib /gbdb/hg38/multiz30way/phyloP30way.wib time hgLoadWiggle -pathPrefix=/gbdb/hg38/multiz30way hg38 \ phyloP30way phyloP30way.wig # real 0m30.538s # use to set trackDb.ra entries for wiggle min and max # and verify table is loaded correctly wigTableStats.sh hg38 phyloP30way # db.table min max mean count sumData # hg38.phyloP30way -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 phyloP30way > 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 phyloP30way track" set xlabel " phyloP30way 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/multiz30way mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way mkdir /hive/data/genomes/hg38/bed/multiz30way/downloads cd /hive/data/genomes/hg38/bed/multiz30way/downloads mkdir multiz30way phastCons30way phyloP30way ######################################################################### ## create upstream refGene maf files cd /hive/data/genomes/hg38/bed/multiz30way/downloads/multiz30way # 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/$MACHTYPE/mafFrags hg38 multiz30way \ stdin stdout \ -orgs=/hive/data/genomes/hg38/bed/multiz30way/species.list \ | gzip -c > upstream${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/multiz30way/downloads/multiz30way 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/multiz30way/maf cd maf ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/maf cd -- ln -s `pwd`/*.maf.gz `pwd`/*.nh `pwd`/*.txt \ /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/multiz30way/ ########################################################################### cd /hive/data/genomes/hg38/bed/multiz30way/downloads/multiz30way grep TREE ../../4d/all.mod | awk '{print $NF}' \ | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ > hg38.30way.nh ~/kent/src/hg/utils/phyloTrees/commonNames.sh hg38.30way.nh \ | ~/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ > hg38.30way.commonNames.nh ~/kent/src/hg/utils/phyloTrees/scientificNames.sh hg38.30way.nh \ | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ > hg38.30way.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/multiz30way 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/multiz30way/ ##################################################################### cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phastCons30way mkdir hg38.30way.phastCons cd hg38.30way.phastCons ln -s ../../../cons/all/downloads/*.wigFix.gz . md5sum *.gz > md5sum.txt cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phastCons30way ln -s ../../cons/all/phastCons30way.bw ./hg38.phastCons30way.bw ln -s ../../cons/all/all.mod ./hg38.phastCons30way.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/phastCons30way/hg38.30way.phastCons cd hg38.30way.phastCons ln -s `pwd`/* /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way/hg38.30way.phastCons cd .. # situation ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phastCons30way ##################################################################### cd /hive/data/genomes/hg38/bed/multiz30way/downloads/phyloP30way mkdir hg38.30way.phyloP cd hg38.30way.phyloP ln -s ../../../consPhyloP/all/downloads/*.wigFix.gz . md5sum *.wigFix.gz > md5sum.txt cd .. ln -s ../../consPhyloP/run.phyloP/all.mod hg38.phyloP30way.mod ln -s ../../consPhyloP/all/phyloP30way.bw hg38.phyloP30way.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/phyloP30way/hg38.30way.phyloP cd hg38.30way.phyloP ln -s `pwd`/* \ /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way/hg38.30way.phyloP cd .. # situation ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \ /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP30way ############################################################################# # 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/multiz30way/pal cd /hive/data/genomes/hg38/bed/multiz30way/pal cat ../species.list | tr '[ ]' '[\n]' > order.list - # this for loop can take hours on a high contig count assembly - # it is just fine on human/hg38, just a few seconds + ### knownCanonical with full CDS + cd /hive/data/genomes/hg38/bed/multiz30way/pal + export mz=multiz30way + 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=multiz30way + 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=multiz30way + 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 $pd + md5sum *.fa.gz > md5sum.txt + + rm -rf exonAA exonNuc + + export mz=multiz30way + export gp=knownCanonical + export db=hg38 + export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$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=multiz30way 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=multiz30way 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.multiz30way.exonAA.fa.gz # -rw-rw-r-- 1 580377720 Nov 6 18:49 knownGene.multiz30way.exonNuc.fa.gz export mz=multiz30way export gp=knownGene export db=hg38 export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments mkdir -p $pd - md5sum *.fa.gz > md5sum.txt ln -s `pwd`/$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/hg38.30way cd /hive/users/hiram/bigWays echo "hg38" > hg38.30way/ordered.list awk '{print $1}' /hive/data/genomes/hg38/bed/multiz30way/30way.distances.txt \ >> hg38.30way/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 hg38.30way/ordered.list # dbDb.sh constructs hg38.30way/XenTro9_30-way_conservation_alignment.html # may need to add new assembly references to srcReference.list and # urlReference.list ./dbDb.sh hg38 30way # sizeStats.pl constructs hg38.30way/XenTro9_30-way_Genome_size_statistics.html # this requires entries in coverage.list for new sequences ./sizeStats.pl hg38 30way # defCheck.pl constructs XenTro9_30-way_conservation_lastz_parameters.html ./defCheck.pl hg38 30way # this constructs the html pages in hg38.30way/: # -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`/multiz30way `pwd`/phastCons30way `pwd`/phyloP30way \ /gbdb/hg38/multiz30way -type f \ > /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList wc -l /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList # 1450 /hive/data/genomes/hg38/bed/multiz30way/downloads/redmine.20216.fileList cd /hive/data/genomes/hg38/bed/multiz30way/downloads hgsql -e 'show tables;' hg38 | grep 30way \ | sed -e 's/^/hg38./;' > redmine.20216.table.list ############################################################################