a13aa5141f01eff76a3e30cf04b9c2a7710d90b7 hiram Mon Jan 11 16:31:50 2021 -0800 ready for pushQ entry refs #26584 diff --git src/hg/makeDb/doc/mm39/multiz35way.txt src/hg/makeDb/doc/mm39/multiz35way.txt index fbe1705..1893d50 100644 --- src/hg/makeDb/doc/mm39/multiz35way.txt +++ src/hg/makeDb/doc/mm39/multiz35way.txt @@ -1,1984 +1,2016 @@ ############################################################################# ## 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/;//; /^ *$/d' \ mm39.35way.nh | xargs echo | sed 's/ //g; s/,/ /g' \ | sed 's/[()]//g; s/,/ /g' | tr '[ ]' '[\n]' > species.list.txt # construct db to name sed translation list: cat species.list.txt | while read DB do hgsql -N -e "select name,organism from dbDb where name=\"${DB}\";" hgcentraltest done | sed -e 's#^#s/#;' | sed -e "s#\t#/#; s/ /_/g;" | sed -e 's#$#/;#' | sed -e 's/\./_/g' \ | sed -e "s#'#_x_#g;" > db.to.name.sed printf "s/GCF_003668045.3/Chinese_hamster/;\n" >> db.to.name.sed sed -f db.to.name.sed mm39.35way.nh | sed -e "s#_x_#'#g; s#X__#X._#;"\ > mm39.35way.commonNames.nh cat mm39.35way.commonNames.nh | sed -e 's/^/# /;' # ((((((((((((((Mouse:0.089509, # Rat:0.096589):0.072773, # Chinese_hamster:0.17):0.08015, # Beaver:0.17):0.05, # Squirrel:0.125468):0.022992, # Guinea_pig:0.175779):0.025746, # (Rabbit:0.114227, # Pika:0.201069):0.101463):0.015313, # ((((((((Human:0.00655, # Chimp:0.00684):0.00122, # Bonobo:0.00784):0.003, # Gorilla:0.008964):0.025204, # Rhesus:0.043601):0.02183, # Marmoset:0.04965):0.05209, # Tarsier:0.1114):0.02052, # Bushbaby:0.13992):0.013494, # (Tree_shrew:0.136203, # Malayan_flying_lemur:0.08):0.054937):0.002):0.020593, # (((Pig:0.12, # (Dolphin:0.064688, # (Cow:0.11, # Sheep:0.085):0.013592):0.045488):0.02, # ((Horse:0.084397, # Chinese_pangolin:0.05):0.017, # (Dog:0.054458, # Hawaiian_monk_seal:0.097):0.069845):0.008727):0.011671, # (Hedgehog:0.221785, # Shrew:0.269562):0.056393):0.021227):0.023664, # (Elephant:0.098929, # Tenrec:0.245936):0.056717):0.234728, # Opossum:0.285786):0.181168, # Chicken:0.509442):0.05, # X._tropicalis:0.347944):0.211354, # Zebrafish:1.201072):0.2, # Lamprey:0.975747); # Use this specification in the phyloGif tool: # http://genome.ucsc.edu/cgi-bin/phyloGif # to obtain a png image for src/hg/htdocs/images/phylo/mm39_35way.png cat species.list.txt | while read DB do hgsql -N -e "select name,scientificName from dbDb where name=\"${DB}\";" hgcentraltest done | sed -e 's#^#s/#;' | sed -e "s#\t#/#; s/ /_/g;" | sed -e 's#$#/;#' | sed -e 's/\./_/g' \ | sed -e "s#'#_x_#g;" > db.to.sciName.sed printf "s/GCF_003668045.3/Cricetulus_griseus/;\n" >> db.to.sciName.sed sed -f db.to.sciName.sed mm39.35way.nh > mm39.35way.scientificNames.nh > mm39.35way.commonNames.nh | $HOME/kent/src/hg/utils/phyloTrees/asciiTree.pl /dev/stdin \ > mm39.35way.scientificNames.nh cat mm39.35way.scientificNames.nh | sed -e 's/^/# /;' # ((((((((((((((Mus_musculus:0.089509, # Rattus_norvegicus:0.096589):0.072773, # Cricetulus_griseus:0.17):0.08015, # Castor_canadensis:0.17):0.05, # Spermophilus_tridecemlineatus:0.125468):0.022992, # Cavia_porcellus:0.175779):0.025746, # (Oryctolagus_cuniculus:0.114227, # Ochotona_princeps:0.201069):0.101463):0.015313, # ((((((((Homo_sapiens:0.00655, # Pan_troglodytes:0.00684):0.00122, # Pan_paniscus:0.00784):0.003, # Gorilla_gorilla_gorilla:0.008964):0.025204, # Macaca_mulatta:0.043601):0.02183, # Callithrix_jacchus:0.04965):0.05209, # Tarsius_syrichta:0.1114):0.02052, # Otolemur_garnettii:0.13992):0.013494, # (Tupaia_belangeri:0.136203, # Galeopterus_variegatus:0.08):0.054937):0.002):0.020593, # (((Sus_scrofa:0.12, # (Tursiops_truncatus:0.064688, # (Bos_taurus:0.11, # Ovis_aries:0.085):0.013592):0.045488):0.02, # ((Equus_caballus:0.084397, # Manis_pentadactyla:0.05):0.017, # (Canis_lupus_familiaris:0.054458, # Neomonachus_schauinslandi:0.097):0.069845):0.008727):0.011671, # (Erinaceus_europaeus:0.221785, # Sorex_araneus:0.269562):0.056393):0.021227):0.023664, # (Loxodonta_africana:0.098929, # Echinops_telfairi:0.245936):0.056717):0.234728, # Monodelphis_domestica:0.285786):0.181168, # Gallus_gallus:0.509442):0.05, # Xenopus_tropicalis:0.347944):0.211354, # Danio_rerio:1.201072):0.2, # Petromyzon_marinus:0.975747); /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 ~/kent/src/hg/makeDb/doc/mm39/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 # try to do these as full chromosomes without the splitting procedure # they will work, they just take a really long time for the big chroms 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: 54 of 54 jobs # CPU time in finished jobs: 1548419s 25806.98m 430.12h 17.92d 0.049 y # IO & Wait Time: 772s 12.87m 0.21h 0.01d 0.000 y # Average job time: 28689s 478.15m 7.97h 0.33d # Longest finished job: 125726s 2095.43m 34.92h 1.46d # Submission to last job: 125739s 2095.65m 34.93h 1.46d ####################################################################### # 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 ... para push # Completed: 54 of 54 jobs # CPU time in finished jobs: 4649s 77.48m 1.29h 0.05d 0.000 y # IO & Wait Time: 346s 5.77m 0.10h 0.00d 0.000 y # Average job time: 93s 1.54m 0.03h 0.00d # Longest finished job: 382s 6.37m 0.11h 0.00d # Submission to last job: 1432s 23.87m 0.40h 0.02d du -hsc result # 141G result # translate those results back to the GCF hub names: cd /hive/data/genomes/mm39/bed/multiz35way mkdir maf printf '#LOOP reverseTrans.sh $(path1) {check out exists+ maf/$(path1).maf} #ENDLOOP ' > template printf '#!/bin/bash set -beEu -o pipefail export C=$1 export R=$2 ~/kent/src/hg/makeDb/mm39/reverseTranslate.pl /hive/data/genomes/asmHubs/refseqBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/GCF_003668045.3_CriGri-PICRH-1.0.chrom.sizes GCF_003668045.3 anno/result/${C}.maf > ${R} ' > reverseTrans.sh chmod +x reverseTrans.sh ls anno/result | sed -e 's/.maf//;' > chr.result.list gensub2 chr.result.list single template reverseTrans.jobList para create reverseTrans.jobList para push # Completed: 54 of 54 jobs # CPU time in finished jobs: 1784s 29.74m 0.50h 0.02d 0.000 y # IO & Wait Time: 1880s 31.33m 0.52h 0.02d 0.000 y # Average job time: 68s 1.13m 0.02h 0.00d # Longest finished job: 245s 4.08m 0.07h 0.00d # Submission to last job: 285s 4.75m 0.08h 0.00d # Load into database rm -f /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. 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 (DONE - 2020-12-22 - 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 (`sed -e "s/GCF_003668045.3 //;" ../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: ncbiRefSeq: 130343, refGene: 47741, xenoRefGene: 197343, # rn6: ensGene: 41078, mgcGenes: 7013, ncbiRefSeq: 69456, refGene: 19160, xenoRefGene: 223156, # casCan1: ensGene: 38514, ncbiRefSeq: 40013, xenoRefGene: 362113, # speTri2: ensGene: 33336, ncbiRefSeq: 41886, xenoRefGene: 446239, # cavPor3: ensGene: 34846, ncbiRefSeq: 44775, refGene: 491, xenoRefGene: 337367 # oryCun2: ensGene: 51853, ncbiRefSeq: 43655, refGene: 1750, xenoRefGene: 345704 # ochPri3: ncbiRefSeq: 26253, xenoRefGene: 313971, # hg38: ensGene: 208239, knownGene: 229647, mgcGenes: 36638, ncbiRefSeq: 170769, refGene: 88819, xenoRefGene: 200365, # panTro6: ncbiRefSeq: 102471, refGene: 2877, xenoRefGene: 245176, # panPan3: ncbiRefSeq: 85047, refGene: 218, xenoRefGene: 246746, # gorGor6: ncbiRefSeq: 61950, refGene: 449, xenoRefGene: 333640, # rheMac10: ensGene: 64228, ncbiRefSeq: 86732, refGene: 6482, xenoRefGene: 243139, # calJac4: ncbiRefSeq: 107273, refGene: 237, xenoRefGene: 256337, # tarSyr2: ensGene: 38314, ncbiRefSeq: 35799, xenoRefGene: 375108, # otoGar3: ensGene: 28565, ncbiRefSeq: 38532, xenoRefGene: 530019, # tupBel1: ensGene: 34727, xenoRefGene: 845862, # galVar1: ncbiRefSeq: 34747, xenoRefGene: 568133, # susScr3: ensGene: 30585, ncbiRefSeq: 66084, refGene: 5345, xenoRefGene: 477106, # turTru2: xenoRefGene: 583163, # bosTau9: ensGene: 43984, ncbiRefSeq: 76369, refGene: 14599, xenoRefGene: 221423, # oviAri4: ncbiRefSeq: 49730, refGene: 1026, xenoRefGene: 230226, # equCab3: ensGene: 59087, ncbiRefSeq: 76580, refGene: 1966, xenoRefGene: 311382, # manPen1: xenoRefGene: 548155, # canFam4: refGene: 2382, xenoRefGene: 238226, # neoSch1: ncbiRefSeq: 29897, xenoRefGene: 446526, # eriEur2: ncbiRefSeq: 29936, xenoRefGene: 315055, # sorAra2: ncbiRefSeq: 23525, xenoRefGene: 469604, # loxAfr3: ensGene: 28847, ncbiRefSeq: 46056, refGene: 23, xenoRefGene: 359460, # echTel2: ncbiRefSeq: 23075, xenoRefGene: 470748, # monDom5: ensGene: 32358, refGene: 1239, xenoRefGene: 256483, # galGal6: ensGene: 39288, ncbiRefSeq: 62170, refGene: 7493, xenoRefGene: 151778, # xenTro9: ensGene: 56323, ncbiRefSeq: 43724, refGene: 8806, xenoRefGene: 164095, # danRer11: ensGene: 59876, ncbiRefSeq: 65219, refGene: 18968, xenoRefGene: 164771, # petMar3: xenoRefGene: 200903, # and for the hub assembly: GCF_003668045.3_CriGri-PICRH-1.0 # wc -l trackData/ncbiRefSeq/process/GCF_003668045.3_CriGri-PICRH-1.0.gp # 61048 trackData/ncbiRefSeq/process/GCF_003668045.3_CriGri-PICRH-1.0.gp # from that summary, use these gene sets: # knownGene - hg38 # ensGene - tupBel1 monDom5 # ncbiRefSeq - mm39 rn6 casCan1 speTri2 cavPor3 oryCun2 ochPri3 panTro6 panPan3 gorGor6 rheMac10 calJac4 tarSyr2 otoGar3 galVar1 susScr3 bosTau9 oviAri4 equCab3 neoSch1 eriEur2 sorAra2 loxAfr3 echTel2 galGal6 xenTro9 danRer11 # xenoRefGene - turTru2 manPen1 canFam4 petMar3 mkdir genes # 1. knownGene: hg38 for DB in hg38 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: 19327 failed: 0 # 2. ensGene: tupBel1 monDom5 for DB in tupBel1 monDom5 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/${DB}.gp.gz done # tupBel1: checked: 29256 failed: 0 # monDom5: checked: 21033 failed: 0 # ncbiRefSeq for the hub: cut -f1 /hive/data/genomes/asmHubs/refseqBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/GCF_003668045.3_CriGri-PICRH-1.0.chrom.sizes | while read C do printf "s/%s/%s/g;\n" "${C}" "`echo $C | sed -e 's/\./v/;'`" done > GCF.name.trans.sed genePredSingleCover /hive/data/genomes/asmHubs/refseqBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/trackData/ncbiRefSeq/process/GCF_003668045.3_CriGri-PICRH-1.0.gp stdout | sed -f GCF.name.trans.sed | gzip -2c > genes/GCF_003668045v3.gp.gz sed -e 's/\./v/;' /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 \ | genePredCheck -chromSizes=stdin genes/GCF_003668045v3.gp.gz # checked: 22354 failed: 0 # 3. ncbiRefSeq - mm39 rn6 casCan1 speTri2 cavPor3 oryCun2 ochPri3 panTro6 panPan3 gorGor6 rheMac10 calJac4 tarSyr2 otoGar3 galVar1 susScr3 bosTau9 oviAri4 equCab3 neoSch1 eriEur2 sorAra2 loxAfr3 echTel2 galGal6 xenTro9 danRer11 for DB in mm39 rn6 casCan1 speTri2 cavPor3 oryCun2 ochPri3 panTro6 \ panPan3 gorGor6 rheMac10 calJac4 tarSyr2 otoGar3 galVar1 susScr3 bosTau9 \ oviAri4 equCab3 neoSch1 eriEur2 sorAra2 loxAfr3 echTel2 galGal6 xenTro9 \ danRer11 do hgsql -N -e "select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds from ncbiRefSeq" ${DB} \ | genePredSingleCover stdin stdout | gzip -2c \ > /dev/shm/${DB}.tmp.gz mv /dev/shm/${DB}.tmp.gz genes/$DB.gp.gz echo -n "# ${DB}: " genePredCheck -db=${DB} genes/${DB}.gp.gz done # mm39: checked: 22051 failed: 0 # rn6: checked: 22857 failed: 0 # casCan1: checked: 21652 failed: 0 # speTri2: checked: 19892 failed: 0 # cavPor3: checked: 19940 failed: 0 # oryCun2: checked: 20276 failed: 0 # ochPri3: checked: 18520 failed: 0 # panTro6: checked: 21380 failed: 0 # panPan3: checked: 22261 failed: 0 # gorGor6: checked: 20581 failed: 0 # rheMac10: checked: 21021 failed: 0 # calJac4: checked: 22183 failed: 0 # tarSyr2: checked: 19968 failed: 0 # otoGar3: checked: 19536 failed: 0 # galVar1: checked: 22794 failed: 0 # susScr3: checked: 24180 failed: 0 # bosTau9: checked: 21001 failed: 0 # oviAri4: checked: 20513 failed: 0 # equCab3: checked: 21079 failed: 0 # neoSch1: checked: 18783 failed: 0 # eriEur2: checked: 19258 failed: 0 # sorAra2: checked: 19160 failed: 0 # loxAfr3: checked: 21061 failed: 0 # echTel2: checked: 18790 failed: 0 # galGal6: checked: 17412 failed: 0 # xenTro9: checked: 21265 failed: 0 # danRer11: checked: 32676 failed: 0 # 3. xenoRefGene - turTru2 manPen1 canFam4 petMar3 for DB in turTru2 manPen1 canFam4 petMar3 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 # turTru2: checked: 36500 failed: 0 # manPen1: checked: 30879 failed: 0 # canFam4: checked: 20127 failed: 0 # petMar3: checked: 10819 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/GCF_003668045v3.gp.gz: 22354 # genes/bosTau9.gp.gz: 20992 # genes/calJac4.gp.gz: 22183 # genes/canFam4.gp.gz: 19154 # genes/casCan1.gp.gz: 21652 # genes/cavPor3.gp.gz: 19938 # genes/danRer11.gp.gz: 29321 # genes/echTel2.gp.gz: 18790 # genes/equCab3.gp.gz: 21079 # genes/eriEur2.gp.gz: 19258 # genes/galGal6.gp.gz: 17404 # genes/galVar1.gp.gz: 22794 # genes/gorGor6.gp.gz: 20579 # genes/hg38.gp.gz: 19310 # genes/loxAfr3.gp.gz: 21061 # genes/manPen1.gp.gz: 26152 # genes/mm39.gp.gz: 22051 # genes/monDom5.gp.gz: 21033 # genes/neoSch1.gp.gz: 18783 # genes/ochPri3.gp.gz: 18520 # genes/oryCun2.gp.gz: 20271 # genes/otoGar3.gp.gz: 19536 # genes/oviAri4.gp.gz: 20508 # genes/panPan3.gp.gz: 22261 # genes/panTro6.gp.gz: 21376 # genes/petMar3.gp.gz: 9982 # genes/rheMac10.gp.gz: 21020 # genes/rn6.gp.gz: 22854 # genes/sorAra2.gp.gz: 19160 # genes/speTri2.gp.gz: 19892 # genes/susScr3.gp.gz: 24043 # genes/tarSyr2.gp.gz: 19968 # genes/tupBel1.gp.gz: 15407 # genes/turTru2.gp.gz: 29711 # genes/xenTro9.gp.gz: 21212 # 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 = $2 cat ../anno/result/${C}.maf | genePredToMafFrames mm39 stdin stdout \ ${G} genes/${G}.gp.gz | gzip > parts/${C}.${G}.mafFrames.gz ' > runOne chmod +x runOne ls ../anno/result | 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).$(root2).mafFrames.gz} #ENDLOOP ' > template mkdir parts gensub2 chr.list gene.list template jobList para -ram=64g create jobList para try ... check ... push # Completed: 1890 of 1890 jobs # CPU time in finished jobs: 68240s 1137.33m 18.96h 0.79d 0.002 y # IO & Wait Time: 62137s 1035.62m 17.26h 0.72d 0.002 y # Average job time: 69s 1.15m 0.02h 0.00d # Longest finished job: 372s 6.20m 0.10h 0.00d # Submission to last job: 1098s 18.30m 0.30h 0.01d # collect all results into one file: cd /hive/data/genomes/mm39/bed/multiz35way/frames time find ./parts -type f | grep -v GCF | while read F do echo "${F}" 1>&2 zcat ${F} done | sort -k1,1 -k2,2n > multiz35wayFrames.bed # real 2m4.953s time find ./parts -type f | grep GCF | while read F do echo "${F}" 1>&2 zcat ${F} | sed -e 's/GCF_003668045v3/GCF_003668045.3/;' done | sort -k1,1 -k2,2n >> multiz35wayFrames.bed # -rw-rw-r-- 1 592159010 Dec 22 09:24 multiz35wayFrames.bed gzip multiz35wayFrames.bed # verify there are frames on everything, should be 35 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 # 35 # 240536 GCF_003668045.3 # 261904 bosTau9 # 266491 calJac4 # 230600 canFam4 # 232036 casCan1 # 240423 cavPor3 # 323912 danRer11 # 229208 echTel2 # 274281 equCab3 # 246825 eriEur2 # 346334 galGal6 # 371538 galVar1 # 245105 gorGor6 # 237059 hg38 # 263806 loxAfr3 # 224191 manPen1 # 200489 mm39 # 348971 monDom5 # 242155 neoSch1 # 226440 ochPri3 # 236903 oryCun2 # 234706 otoGar3 # 296794 oviAri4 # 264590 panPan3 # 263990 panTro6 # 146858 petMar3 # 261855 rheMac10 # 235340 rn6 # 239030 sorAra2 # 230420 speTri2 # 257781 susScr3 # 231443 tarSyr2 # 196941 tupBel1 # 258704 turTru2 # 322154 xenTro9 # load the resulting file ssh hgwdev cd /hive/data/genomes/mm39/bed/multiz35way/frames time hgLoadMafFrames mm39 multiz35wayFrames multiz35wayFrames.bed.gz # real 1m0.040s hgsql -e 'select count(*) from multiz35wayFrames;' mm39 # +----------+ # | count(*) | # +----------+ # | 8929813 | # +----------+ time featureBits -countGaps mm39 multiz35wayFrames # 60020650 bases of 2728222451 (2.200%) in intersection # real 0m43.619s # 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 ncbiRefSeq where cdsEnd > cdsStart;" mm39 \ | egrep -E -v "chrM|chrUn|random|_alt" > ncbiRefSeq.gp wc -l *.gp # 95199 ncbiRefSeq.gp genePredCheck -db=mm39 ncbiRefSeq.gp # checked: 92405 failed: 0 # verify it is only on the chroms: cut -f2 ncbiRefSeq.gp | sort | uniq -c | sort -rn | sed -e 's/^/ # /;' # 7748 chr2 # 7617 chr7 # 6852 chr11 # 5889 chr4 # 5843 chr1 # 5810 chr5 # 5514 chr9 # 4700 chr6 # 4477 chr8 # 4357 chr10 # 4310 chr17 # 4158 chr3 # 3615 chr14 # 3530 chr15 # 3479 chrX # 3254 chr12 # 2968 chr13 # 2952 chr16 # 2718 chr19 # 2301 chr18 # 313 chrY genePredSingleCover ncbiRefSeq.gp stdout | sort > ncbiRefSeqNP.gp wc -l ncbiRefSeqNP.gp # 21990 ncbiRefSeqNP.gp genePredCheck -db=mm39 ncbiRefSeqNP.gp # checked: 21990 failed: 0 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}' $r/4d/ncbiRefSeqNP.gp | sed -e "s/\t$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: 21 of 21 jobs # CPU time in finished jobs: 5711s 95.18m 1.59h 0.07d 0.000 y # IO & Wait Time: 62s 1.03m 0.02h 0.00d 0.000 y # Average job time: 275s 4.58m 0.08h 0.00d # Longest finished job: 470s 7.83m 0.13h 0.01d # Submission to last job: 471s 7.85m 0.13h 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 293090 Dec 22 11:46 chrY.mfa #want comma-less species.list time /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/msa_view \ --aggregate "`sed -e 's/GCF_003668045.3/GCF_003668045v3/;' \ ../species.list`" mfa/*.mfa | sed s/"> "/">"/ > 4d.all.mfa # real 0m3.182s # check they are all in there: grep "^>" 4d.all.mfa | wc -l # 35 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 | sed -e 's/GCF_003668045.3/GCF_003668045v3/;' \ > 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 67m7.237s mv phyloFit.mod all.mod grep TREE all.mod TREE: ((((((((((((((mm39:0.0843874,rn6:0.0899985):0.0657921, GCF_003668045v3:0.106248):0.151018,casCan1:0.135335):0.0230996, speTri2:0.144923):0.00521622,cavPor3:0.232945):0.026955, (oryCun2:0.11389,ochPri3:0.195179):0.105379):0.0128213, ((((((((hg38:0.0109653,panTro6:0.00222548):0.00206435, panPan3:0.00221569):0.00629185,gorGor6:0.00877389):0.0221025, rheMac10:0.0361164):0.0217292,calJac4:0.0658044):0.0586954, tarSyr2:0.140238):0.0112568,otoGar3:0.155854):0.0148223, (tupBel1:0.182689,galVar1:0.106299):0.00938657):0.00641):0.0206, (((susScr3:0.119945,(turTru2:0.0637542,(bosTau9:0.0311355, oviAri4:0.0369141):0.0938814):0.0195077):0.0461252, ((equCab3:0.105047,manPen1:0.137597):0.00716862, (canFam4:0.0869943,neoSch1:0.0695671):0.0650575):0.00523737):0.0112043, (eriEur2:0.221845,sorAra2:0.280481):0.0694824):0.0210386):0.0285152, (loxAfr3:0.103064,echTel2:0.240863):0.0478413):0.237009, monDom5:0.34975):0.214304,galGal6:0.444509):0.287968, xenTro9:0.766181):0.454886,danRer11:0.852917):0.44051,petMar3:0.44051); # 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.//; s/GCF_003668045v3/GCF_003668045.3/;" | sort > mm39.dists # printing out the 'original', the 'new' the 'difference' and # percent difference/delta echo "# sequence old dist new dist difference per-cent diff" join original.dists mm39.dists | awk '{ printf "#\t%s\t%8.6f\t%8.6f\t%8.6f\t%5.2f\n", $1, $2, $3, $2-$3, 100*($2-$3)/$3 }' | sort -k4n # sequence old dist new dist difference per-cent diff # rn6 0.186098 0.174386 0.011712 6.72 # GCF_003668045.3 0.332282 0.256428 0.075854 29.58 # casCan1 0.412432 0.436532 -0.024100 -5.52 # speTri2 0.417900 0.469220 -0.051320 -10.94 # galVar1 0.493420 0.491385 0.002035 0.41 # panPan3 0.502461 0.512813 -0.010352 -2.02 # gorGor6 0.500585 0.513080 -0.012495 -2.44 # panTro6 0.502681 0.514887 -0.012206 -2.37 # rheMac10 0.510018 0.518320 -0.008302 -1.60 # hg38 0.502391 0.523627 -0.021236 -4.06 # calJac4 0.494237 0.526279 -0.032042 -6.09 # equCab3 0.520098 0.539586 -0.019488 -3.61 # tarSyr2 0.503897 0.542017 -0.038120 -7.03 # otoGar3 0.511897 0.546376 -0.034479 -6.31 # turTru2 0.540150 0.551520 -0.011370 -2.06 # neoSch1 0.585546 0.561994 0.023552 4.19 # cavPor3 0.491203 0.562458 -0.071255 -12.67 # tupBel1 0.549623 0.567775 -0.018152 -3.20 # loxAfr3 0.556386 0.569310 -0.012924 -2.27 # manPen1 0.485701 0.572136 -0.086435 -15.11 # oryCun2 0.556860 0.575737 -0.018877 -3.28 # canFam4 0.543004 0.579422 -0.036418 -6.29 # susScr3 0.549974 0.588203 -0.038229 -6.50 # bosTau9 0.599054 0.612782 -0.013728 -2.24 # oviAri4 0.574054 0.618561 -0.044507 -7.20 # ochPri3 0.643702 0.657026 -0.013324 -2.03 # eriEur2 0.676481 0.702256 -0.025775 -3.67 # echTel2 0.703393 0.707109 -0.003716 -0.53 # sorAra2 0.724258 0.760892 -0.036634 -4.81 # monDom5 0.921254 1.005164 -0.083910 -8.35 # galGal6 1.326078 1.314227 0.011851 0.90 # xenTro9 1.214580 1.923867 -0.709287 -36.87 # danRer11 2.279062 2.465489 -0.186427 -7.56 # petMar3 2.253737 2.493592 -0.239855 -9.62 ######################################################################### # phastCons 35-way (DONE - 2020-12-22 - 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 printf '#LOOP doSplit.csh $(root1) {check out line+ $(root1).done} #ENDLOOP ' > template # 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: 54 of 54 jobs # CPU time in finished jobs: 24295s 404.91m 6.75h 0.28d 0.001 y # IO & Wait Time: 1111s 18.52m 0.31h 0.01d 0.000 y # Average job time: 470s 7.84m 0.13h 0.01d # Longest finished job: 2724s 45.40m 0.76h 0.03d # Submission to last job: 2765s 46.08m 0.77h 0.03d # 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 # 930 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: 930 of 930 jobs # CPU time in finished jobs: 22874s 381.23m 6.35h 0.26d 0.001 y # IO & Wait Time: 6698s 111.64m 1.86h 0.08d 0.000 y # Average job time: 32s 0.53m 0.01h 0.00d # Longest finished job: 49s 0.82m 0.01h 0.00d # Submission to last job: 200s 3.33m 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 0m43.805s # -rw-rw-r-- 1 164925477 Dec 22 14:02 tmpMostConserved.bed time /cluster/bin/scripts/lodToBedScore tmpMostConserved.bed \ > mostConserved.bed # real 0m26.890s # -rw-rw-r-- 1 169120947 Dec 22 14:04 mostConserved.bed # load into database ssh hgwdev cd /hive/data/genomes/mm39/bed/multiz35way/cons/all time hgLoadBed mm39 phastConsElements35way mostConserved.bed # Read 4829247 elements of size 5 from mostConserved.bed # real 0m36.697s # Try for 5% overall cov, and 70% CDS cov # --rho 0.3 --expected-length 45 --target-coverage 0.3 time featureBits mm39 -enrichment ncbiRefSeq:cds phastConsElements35way # ncbiRefSeq:cds 1.408%, phastConsElements35way 5.679%, both 0.993%, cover 70.51%, enrich 12.42x # real 0m31.631s time featureBits mm39 -enrichment refGene:cds phastConsElements35way # refGene:cds 1.333%, phastConsElements35way 5.679%, both 0.972%, cover 72.87%, enrich 12.83x # real 0m24.183s # 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 15m34.013s # 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 6m57.150s du -hsc *.wi? # 1.9G phastCons35way.wib # 223M 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=29661: VmPeak: 22610628 kB # real 21m44.557s # -rw-rw-r-- 1 4567105688 Dec 22 16:47 phastCons35way.bw bigWigInfo phastCons35way.bw version: 4 isCompressed: yes isSwapped: 0 primaryDataSize: 3,226,958,317 primaryIndexSize: 75,088,076 zoomLevels: 10 chromCount: 54 basesCovered: 2,035,330,949 mean: 0.124503 min: 0.000000 max: 1.000000 # 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 0m18.870s time wigTableStats.sh mm39 phastCons35way # db.table min max mean count sumData # mm39.phastCons35way 0 1 0.124503 2035330949 2.53404e+08 # stdDev viewLimits # 0.262545 viewLimits=0:1 # real 0m8.782s # 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 1m30.048s # create plot of histogram: XXX - need to update this gnuplot definition: 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 (DONE - 2020-12-22 - 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: 54 of 54 jobs # CPU time in finished jobs: 25321s 422.01m 7.03h 0.29d 0.001 y # IO & Wait Time: 843s 14.06m 0.23h 0.01d 0.000 y # Average job time: 485s 8.08m 0.13h 0.01d # Longest finished job: 2873s 47.88m 0.80h 0.03d # Submission to last job: 2931s 48.85m 0.81h 0.03d # 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: 0.219062 0.338786 0.207231 0.234921 grep BACKGROUND ../../4d/all.mod | awk '{printf "%0.3f\n", $3 + $4}' # 0.546 /cluster/bin/phast.build/cornellCVS/phast.2010-12-30/bin/modFreqs \ ../../4d/all.mod 0.546 > 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: 2699 of 2699 jobs # CPU time in finished jobs: 839140s 13985.67m 233.09h 9.71d 0.027 y # IO & Wait Time: 17961s 299.35m 4.99h 0.21d 0.001 y # Average job time: 318s 5.29m 0.09h 0.00d # Longest finished job: 657s 10.95m 0.18h 0.01d # Submission to last job: 3669s 61.15m 1.02h 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 30m48.598s du -hsc downloads # 3.4G 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 -XXX - running - Tue Dec 22 18:30:43 PST 2020 egrep "real|VmPeak" bigWig.log - # pid=66292: VmPeak: 33751268 kB - # real 43m40.194s - + # pid=123418: VmPeak: 22609988 kB + # real 22m26.776s bigWigInfo phyloP35way.bw | sed -e 's/^/# /;' # version: 4 # isCompressed: yes # isSwapped: 0 # primaryDataSize: 4,660,484,132 # primaryIndexSize: 75,089,444 # zoomLevels: 10 # chromCount: 53 # basesCovered: 2,035,330,611 # mean: 0.110677 # min: -13.709000 # max: 4.643000 # std: 0.833332 # encode those files into wiggle data time (zcat downloads/*.wigFix.gz \ | wigEncode stdin phyloP35way.wig phyloP35way.wib) # Converted stdin, upper limit 4.64, lower limit -13.71 # real 8m41.899s # -rw-rw-r-- 1 2035330611 Dec 22 18:40 phyloP35way.wib # -rw-rw-r-- 1 239980863 Dec 22 18:40 phyloP35way.wig du -hsc *.wi? # 1.9G phyloP35way.wib # 229M 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 0m15.232s # 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 -13.709 4.643 0.110677 2035330611 2.25264e+08 # stdDev viewLimits # 0.833332 viewLimits=-4.05598:4.27734 # that range is: 13.709+4.643 = 18.352 for hBinSize=0.018352 # Create histogram to get an overview of all the data time hgWiggle -doHistogram \ -hBinSize=0.018352 -hBinCount=1000 -hMinVal=-20 -verbose=2 \ -db=mm39 phyloP35way > histogram.data 2>&1 # real 1m14.295s XXX - ready to graph - Tue Dec 22 21:28:59 PST 2020 # 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 + + # Brian had to fix mafFrags so it could work with the assembly GCF + # identifier + # bash script #!/bin/sh export geneTbl="ncbiRefSeq" 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 -XXX - running - Wed Dec 23 14:36:49 PST 2020 - # real 88m40.730s - --rw-rw-r-- 1 52659159 Nov 6 11:46 upstream300.ncbiRefSeq.maf.gz --rw-rw-r-- 1 451126665 Nov 6 12:15 upstream2000.ncbiRefSeq.maf.gz --rw-rw-r-- 1 1080533794 Nov 6 12:55 upstream5000.ncbiRefSeq.maf.gz + # real 117m33.236s + +-rw-rw-r-- 1 96310644 Jan 4 17:04 upstream300.ncbiRefSeq.maf.gz +-rw-rw-r-- 1 948130770 Jan 4 17:41 upstream2000.ncbiRefSeq.maf.gz +-rw-rw-r-- 1 2032740393 Jan 4 18:48 upstream5000.ncbiRefSeq.maf.gz + + # verify sanity: + zgrep "^s " upstream300.ncbiRefSeq.maf.gz | awk '{print $2}' \ + | sort | uniq -c | sort -rn | less + + # they all have the same counts, followed by single gene names: + 89641 xenTro9 + 89641 turTru2 + 89641 tupBel1 + 89641 tarSyr2 + 89641 susScr3 +... + 89641 casCan1 + 89641 canFam4 + 89641 calJac4 + 89641 bosTau9 + 89641 GCF_003668045.3 + 1 XM_982184.5 + 1 XM_981747.8 + 1 XM_981711.5 + 1 XM_981599.4 + 1 XM_977914.8 +... etc ... + + # same pattern seen with the 2000 and 5000 upstreams + zgrep "^s " upstream2000.ncbiRefSeq.maf.gz | awk '{print $2}' \ + | sort | uniq -c | sort -rn | less + + zgrep "^s " upstream5000.ncbiRefSeq.maf.gz | awk '{print $2}' \ + | sort | uniq -c | sort -rn | less ###################################################################### ## compress the maf files cd /hive/data/genomes/mm39/bed/multiz35way/downloads/multiz35way mkdir maf time rsync -a -P ../../maf/ ./maf/ # real 12m9.290s du -hscL maf/ ../../maf/ # 141G maf/ # 141G ../../maf/ cd maf time gzip *.maf & -XXX - running - Wed Dec 23 14:55:47 PST 2020 - # real 81m10.239s + # about an hour du -hscL maf ../../maf/ - # 18G maf + # 16G maf + # 141G ../../maf/ cd maf - md5sum *.maf.gz *.nh > md5sum.txt + md5sum *.maf.gz > 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 sed -f ../../db.to.name.sed mm39.35way.nh \ | sed -e "s#_x_#'#g; s#X__#X._#;" > mm39.35way.commonNames.nh sed -f ../../db.to.sciName.sed mm39.35way.nh \ > 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 -hscL ./maf ../../maf # 18G ./maf # 156G ../../maf -XXX # obtain the README.txt from danRer10/multiz12way 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 -XXX - # obtain the README.txt from mm39/phastCons20way and update for this + # obtain the README.txt from danRer10/phastCons12way 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 -XXX - # obtain the README.txt from mm39/phyloP20way and update for this + # obtain the README.txt from danRer10/phyloP12way and update for this + # situation 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) +# hgPal downloads (DONE - 2020-12-23 - Hiram) # FASTA from 35-way for ncbiRefSeq, 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 # ncbiRefSeq export mz=multiz35way export gp=ncbiRefSeq 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 18m43.962s export mz=multiz35way export gp=ncbiRefSeq time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \ | gzip -c > $gp.$mz.exonAA.fa.gz # real 2m0.962s time find ./exonNuc -type f | grep exonNuc.fa.gz | xargs zcat \ | gzip -c > $gp.$mz.exonNuc.fa.gz # real 10m12.351s # -rw-rw-r-- 1 906052407 Dec 23 16:34 ncbiRefSeq.multiz35way.exonAA.fa.gz # -rw-rw-r-- 1 1596566489 Dec 23 16:53 ncbiRefSeq.multiz35way.exonNuc.fa.gz export mz=multiz35way export gp=ncbiRefSeq export db=mm39 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/ rm -rf exonAA exonNuc ############################################################################# -# wiki page for 35-way (TBD - 2017-11-06 - Hiram) +# wiki page for 35-way (DONE - 2021-01-11 - 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 + # Updated this script to work with the GCF accession and finding relevant + # data from the assembly hub files ./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 +# -rw-rw-r-- 1 17957 Jan 4 17:56 Mm39_35-way_conservation_alignment.html +# -rw-rw-r-- 1 11991 Jan 4 17:58 Mm39_35-way_conservation_lastz_parameters.html +# -rw-rw-r-- 1 23297 Jan 11 14:58 Mm39_35-way_Genome_size_statistics.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 +# Mm39_35-way_Genome_size_statistics.html +# Mm39_35-way_conservation_alignment.html +# Mm39_35-way_conservation_lastz_parameters.html # when you view the first one you enter, it will have links to the # missing two. ############################################################################ -# pushQ readmine (TBD - 2017-11-07 - Hiram) +# pushQ readmine (TBD - 2021-01-11 - Hiram) +XXX - ready - Mon Jan 11 16:30:45 PST 2021 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 ############################################################################