7eb8b7de9987604dde002fcf9c7cb4f4b38e3d3e hiram Mon Nov 25 15:43:05 2019 -0800 begin build of regenCho1 refs #24524 diff --git src/hg/makeDb/doc/regenCho1/initialBuild.txt src/hg/makeDb/doc/regenCho1/initialBuild.txt new file mode 100644 index 0000000..594b0dc --- /dev/null +++ src/hg/makeDb/doc/regenCho1/initialBuild.txt @@ -0,0 +1,1070 @@ +# for emacs: -*- mode: sh; -*- + +# This file describes browser build for the regenCho1 + +# Can use existing photograph (otherwise find one before starting here) + +######################################################################### +# Initial steps, use existing photograph (DONE - 2019-11-18 - Hiram) + +# To start this initialBuild.txt document, from a previous assembly document: + +mkdir ~/kent/src/hg/makeDb/doc/regenCho1 +cd ~/kent/src/hg/makeDb/doc/regenCho1 + +sed -e 's/galGal6/regenCho1/g; s/GalGal6/RegenCho1/g; s/DONE/TBD/g;' \ + ../galGal6/initialBuild.txt > initialBuild.txt + +mkdir -p /hive/data/genomes/regenCho1/regeneron +# sequences were obtained via email instructions from Regeneron +# downloaded from a URl for their secure situation +-rw-r--r-- 1 642308119 Nov 16 21:13 regen.cho.zip +# unzipped (with a few tricks) into the files: +-rw-rw-r-- 1 2404315688 Nov 16 13:20 REGN_CHO_HYBRID_SCAFFOLD.fasta +-rw-rw-r-- 1 127348249 Nov 16 13:21 REGN_CHO_CONTIGS.fasta +-rw-rw-r-- 1 954479 Nov 16 13:22 REGN_CHO.agp +# tricks: When you unzip the file, you obtain: +-rw-rw-r-- 1 169 Nov 17 05:11 md5sum.txt +-rw-rw-r-- 1 642893273 Nov 17 05:11 REGN_CHO_ASSM.tgz +# the file named .tgz is a gzipped file tar image, you need to: +# mv REGN_CHO_ASSM.tgz REGN_CHO_ASSM.tar.gz +# gunzip REGN_CHO_ASSM.tar.gz +# tar xvf REGN_CHO_ASSM.tar + +# check assembly size for later reference: +faSize REGN_CHO_HYBRID_SCAFFOLD.fasta +# 2404312997 bases (265206282 N's 2139106715 real 2134987163 upper +# 4119552 lower) in 113 sequences in 1 files +# Total size: mean 21277106.2 sd 48948367.5 min 65387 (Super-Scaffold_100188) +# max 240360982 (Super-Scaffold_100001) median 796941 +# %0.17 masked total, %0.19 masked real + +faSize REGN_CHO_CONTIGS.fasta +# 127192052 bases (0 N's 127192052 real 111817586 upper 15374466 lower) +# in 7771 sequences in 1 files +# Total size: mean 16367.5 sd 16086.3 min 4 (011634F_pilon_obj) +# max 493946 (001235F_pilon_obj) median 11822 +# %12.09 masked total, %12.09 masked real + +# check for duplicate sequence: +faToTwoBit REGN_CHO_HYBRID_SCAFFOLD.fasta REGN_CHO_CONTIGS.fasta test.2bit +# should be silent: +twoBitDup test.2bit + +# Can use existing photograph +cd /hive/data/genomes/regenCho1 +cp -p ../criGriChoV2/photoReference.txt . + +cp -p ../rn6/photoReference.txt . +cat photoReference.txt +photoCreditURL https://commons.wikimedia.org/wiki/File:Cho_cells_adherend2.jpg +photoCreditName WikiMedia Commons: Alcibiades + +############################################################################# +# establish config.ra file (DONE - Hiram - 2019-11-25) + cd /hive/data/genomes/regenCho1 + # copy the criGriChoV2 file and edit: + cp -p ../criGriChoV2/criGriChoV2.config.ra regenCho1.config.ra + + + cat regenRn9.config.ra +# config parameters for makeGenomeDb.pl: +db regenCho1 +clade mammal +scientificName Cricetulus griseus +commonName Chinese hamster +assemblyDate Nov. 2019 +assemblyLabel Regeneron CHOv1 +assemblyShortLabel regenCho1 +orderKey 3347 +# including NC_007936.1 in the ucsc/chrM.* files from criGriChoV2 +mitoAcc none +fastaFiles /hive/data/genomes/regenCho1/ucsc/*.fa.gz +agpFiles /hive/data/genomes/regenCho1/ucsc/*.agp +# qualFiles none +dbDbSpeciesDir criGri +photoCreditURL https://commons.wikimedia.org/wiki/File:Cho_cells_adherend2.jpg +photoCreditName WikiMedia Commons: Alcibiades +ncbiGenomeId 2791 +ncbiAssemblyId 1422381 +ncbiAssemblyName CHOK1S_HZDv1 +ncbiBioProject PRJEB21211 +ncbiBioSample SAMEA104116709 +genBankAccessionID GCA_900186095.1 +taxId 10029 + + # compare with previous version to see if it is sane: + diff regenCho1.config.ra ../criGriChoV2/criGriChoV2.config.ra + +############################################################################# +# setup UCSC named files (DONE - 2019-11-25 - Hiram) + + mkdir /hive/data/genomes/regenCho1/ucsc + cd /hive/data/genomes/regenCho1/ucsc + + # limit to contigs only 100 bases and larger: + + awk '$2 > 99' ../regeneron/REGN_CHO.chrom.sizes \ + > limit.sizes + + cut -f1 limit.sizes | sort > allowed.names + + # running this script to get the contig names shorter + # result of this script output into: ucsc.regeneron.name.translate + + printf '#!/usr/bin/env perl + +use strict; +use warnings; + +open (FH, "<allowed.names") or die "can not read allowed.names"; +while (my $line = <FH>) { + chomp $line; + my $ucscName = $line; + if ($ucscName =~ m/^Super-Scaffold/) { + $ucscName =~ s/Super-Scaffold_/ss/; + } elsif ($ucscName =~ m/_pilon_obj$/) { + $ucscName =~ s/_pilon_obj//; + $ucscName =~ s/^/pi/; + } elsif ($ucscName =~ m/pilon_subseq/) { + if ($ucscName =~ m/000052F_pilon_subseq/) { + $ucscName =~ s/32403:237079_obj//; + $ucscName =~ s/027473:1032013_obj//; + $ucscName =~ s/_pilon_subseq//; + } else { + $ucscName =~ s/_pilon_subseq_.*//; + } + $ucscName =~ s/^/pisub/; + } else { + die "can not recognize $ucscName"; + } + printf "%%s\\t%%s\\n", $ucscName, $line; +} +close (FH); +' > nameMangle.pl + + chmod +x nameMangle.pl + + ./nameMangle.pl > ucsc.regeneron.name.translate + # three of the names had to be fixed up that came out as a duplicates +# pisub002451F 002451F_pilon_subseq_1:60219_obj +# pisub002451F 002451F_pilon_subseq_60220:143470_obj +# pisub002349F 002349F_pilon_subseq_113319:159808_obj +# pisub002349F 002349F_pilon_subseq_93081:113318_obj +# pisub002822F 002822F_pilon_subseq_1:48280_obj +# pisub002822F 002822F_pilon_subseq_48281:109600_obj + + # to become: +# pisub002451Fa 002451F_pilon_subseq_1:60219_obj +# pisub002451Fb 002451F_pilon_subseq_60220:143470_obj +# pisub002349Fa 002349F_pilon_subseq_113319:159808_obj +# pisub002349Fb 002349F_pilon_subseq_93081:113318_obj +# pisub002822Fa 002822F_pilon_subseq_1:48280_obj +# pisub002822Fb 002822F_pilon_subseq_48281:109600_obj + + + # this script translated the contig names in the fasta file + # result into: | gzip -c > ucsc.fa.gz + + printf '#!/usr/bin/env perl + +use strict; +use warnings; + +my %%regenToUcsc; # key is Regeneron name, value is UCSC name + +open (FH, "<ucsc.regeneron.name.translate") or die "can not read ucsc.regeneron.name.translate"; +while (my $line = <FH>) { + chomp $line; + my ($ucsc, $regen) = split('"'"'\\s+'"'"', $line); + die "regen name already seen $regen" if (defined($regenToUcsc{$regen})); + $regenToUcsc{$regen} = $ucsc; +} +close (FH); + +my $skipping = 0; + +open (FH, "cat ../regeneron/REGN_CHO_HYBRID_SCAFFOLD.fasta ../regeneron/REGN_CHO_CONTIGS.fasta|") or die "can not read the fasta files"; +while (my $line = <FH>) { + chomp $line; + if ($line =~ m/^>/) { + $line =~ s/>//; + if (!defined($regenToUcsc{$line})) { + $skipping = 1; + } else { + printf ">%%s\\n", $regenToUcsc{$line}; + $skipping = 0; + } + } else { + if ($skipping) { + next; + } else { + printf "%%s\\n", $line; + } + } +} +close (FH); +' > translateFasta.pl + + + chmod +x translateFasta.pl + + time ./translateFasta.pl | gzip -c > ucsc.fa.gz + # using chrM from criGriChoV2 + cp -p ../../criGriChoV2/ucsc/chrM.agp . + cp -p ../../criGriChoV2/ucsc/chrM.fa.gz . + + # verify the resulting fasta is sane, and no duplicates: + + faToTwoBit ucsc.fa.gz chrM.fa.gz test.2bit + twoBitDup test.2bit + # no output is a good result, otherwise, would have to eliminate duplicates + # the scripts creating the fasta here will be using this refseq.2bit file + # remove it later + + # what kind of gaps are there + twoBitInfo -nBed test.2bit test.nBed + + awk '{print $3-$2,$0}' test.nBed | sort -n | head + # 5 ss100002 204423915 204423920 + # 6 ss100011 48606414 48606420 + awk '{print $3-$2,$0}' test.nBed | sort -n | tail + # 117669 ss100003 119385162 119502831 + # 165458 ss100001 75253875 75419333 + + awk '{print $3-$2}' test.nBed | ave stdin +Q1 2137.000000 +median 3822.000000 +Q3 6640.500000 +average 5128.624123 +min 5.000000 +max 165458.000000 +count 51711 +total 265206282.000000 +standard deviation 4674.221642 + + twoBitToFa test.2bit stdout \ + | hgFakeAgp -minContigGap=1 -singleContigs stdin fake.agp + checkAgpAndFa fake.agp test.2bit 2>&1 | tail -4 + # All AGP and FASTA entries agree - both files are valid + + twoBitToFa test.2bit stdout | faSize stdin +# 2531519022 bases (265206282 N's 2266312740 real 2246820852 upper +# 19491888 lower) in 7812 sequences in 1 files +# Total size: mean 324055.2 sd 6387461.2 min 105 (pi011564F) +# max 240360982 (ss100001) median 12236 + + # no longer need the temporary 2bit file + rm test.2bit test.nBed + +############################################################################# +# Initial database build (DONE - 2019-11-25 - Hiram) + + # verify sequence and AGP are OK: + time (makeGenomeDb.pl -stop=db regenCho1.config.ra -workhorse=hgwdev) \ + > db.log 2>&1 + # real 16m7.888s + + # finish it off: + time (makeGenomeDb.pl -continue=dbDb regenCho1.config.ra -workhorse=hgwdev) \ + > dbDb.log 2>&1 + # real 0m8.473s + + # check in the trackDb files created in TemporaryTrackDbCheckout/ + # and add regenCho1 to trackDb/makefile + + # temporary symlink until masked sequence is available + cd /hive/data/genomes/regenCho1 + ln -s `pwd`/regenCho1.unmasked.2bit /gbdb/regenCho1/regenCho1.2bit + +############################################################################## +# cpgIslands on UNMASKED sequence (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/cpgIslandsUnmasked + cd /hive/data/genomes/regenCho1/bed/cpgIslandsUnmasked + + time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ + -tableName=cpgIslandExtUnmasked \ + -maskedSeq=/hive/data/genomes/regenCho1/regenCho1.unmasked.2bit \ + -workhorse=hgwdev -smallClusterHub=ku regenCho1) > do.log 2>&1 +XXX - running - Mon Nov 25 15:18:59 PST 2019 + # real 3m46.939s + + cat fb.regenCho1.cpgIslandExtUnmasked.txt + # 11929440 bases of 2534810853 (0.471%) in intersection + +############################################################################# +# cytoBandIdeo - (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/cytoBand + cd /hive/data/genomes/regenCho1/bed/cytoBand + makeCytoBandIdeo.csh regenCho1 + +############################################################################# +# run up idKeys files for chromAlias/ncbiRefSeq (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/idKeys + cd /hive/data/genomes/regenCho1/bed/idKeys + + time (doIdKeys.pl \ + -twoBit=/hive/data/genomes/regenCho1/regenCho1.unmasked.2bit \ + -buildDir=`pwd` regenCho1) > do.log 2>&1 & +XXX - running - Mon Nov 25 15:20:21 PST 2019 + # real 0m47.105s + + cat regenCho1.keySignature.txt + # 7850e2d5dabb6134fdc9d7083f1a3a54 + +############################################################################# +# gapOverlap (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/gapOverlap + cd /hive/data/genomes/regenCho1/bed/gapOverlap + time (doGapOverlap.pl \ + -twoBit=/hive/data/genomes/regenCho1/regenCho1.unmasked.2bit regenCho1 ) \ + > do.log 2>&1 & +XXX - running - Mon Nov 25 15:21:16 PST 2019 + # real 1m51.246s + + # there are 7 items found: + wc -l bed.tab + # 7 bed.tab + + cat fb.regenCho1.gapOverlap.txt + # 5912 bases of 2762428432 (0.000%) in intersection + +############################################################################# +# tandemDups (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/tandemDups + cd /hive/data/genomes/regenCho1/bed/tandemDups + time (~/kent/src/hg/utils/automation/doTandemDup.pl \ + -twoBit=/hive/data/genomes/regenCho1/regenCho1.unmasked.2bit regenCho1) \ + > do.log 2>&1 & +XXX - running - Mon Nov 25 15:24:00 PST 2019 + # real 369m58.055s + + cat fb.regenCho1.tandemDups.txt + # 86298981 bases of 2762428432 (3.124%) in intersection + + bigBedInfo regenCho1.tandemDups.bb | sed -e 's/^/# /;' +# version: 4 +# fieldCount: 13 +# hasHeaderExtension: yes +# isCompressed: yes +# isSwapped: 0 +# extraIndexCount: 0 +# itemCount: 1,039,087 +# primaryDataSize: 27,356,255 +# primaryIndexSize: 178,160 +# zoomLevels: 9 +# chromCount: 3504 +# basesCovered: 1,365,621,612 +# meanDepth (of bases covered): 6.439341 +# minDepth: 1.000000 +# maxDepth: 307.000000 +# std of depth: 12.663540 + +######################################################################### +# ucscToINSDC and ucscToRefSeq table/track (TBD - 2019-11-25 - Hiram) + # construct idKeys for the refseq sequence + mkdir /hive/data/genomes/regenCho1/refseq/idKeys + cd /hive/data/genomes/regenCho1/refseq/idKeys + faToTwoBit ../GCF_000002315.5_GRCg6a_genomic.fna.gz regenCho1.refSeq.2bit + + time (doIdKeys.pl -buildDir=`pwd` \ + -twoBit=`pwd`/regenCho1.refSeq.2bit refseqRegenCho1) > do.log 2>&1 & + # real 0m48.786s + + cat refseqRegenCho1.keySignature.txt + # 7850e2d5dabb6134fdc9d7083f1a3a54 + + # and the genbank sequence needs keys too: + mkdir /hive/data/genomes/regenCho1/refseq/idKeysGenbank + cd /hive/data/genomes/regenCho1/refseq/idKeysGenbank + faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_other/Gallus_gallus/all_assembly_versions/GCA_000002315.5_GRCg6a/GCA_000002315.5_GRCg6a_genomic.fna.gz regenCho1.genbank.2bit + + time (doIdKeys.pl -buildDir=`pwd` \ + -twoBit=`pwd`/regenCho1.genbank.2bit genbankRegenCho1) > do.log 2>&1 & + + cat genbankRegenCho1.keySignature.txt + # a20fdad3318d371fcb34fcc66bab3752 + + mkdir /hive/data/genomes/regenCho1/bed/chromAlias + + join -t$'\t' ../idKeys/regenCho1.idKeys.txt \ + ../../refseq/idKeysGenbank/genbankRegenCho1.idKeys.txt | cut -f2- \ + | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \ + | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \ + | sort -k1,1 -k2,2n > ucscToINSDC.bed + + join -t$'\t' ../idKeys/regenCho1.idKeys.txt \ + ../../refseq/idKeys/refseqRegenCho1.idKeys.txt | cut -f2- \ + | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \ + | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \ + | sort -k1,1 -k2,2n > ucscToRefSeq.bed + + # should be same line counts throughout: + wc -l * ../../chrom.sizes + # 463 ucscToINSDC.bed + # 464 ucscToRefSeq.bed + # 464 ../../chrom.sizes + + # need to find the accession for the INSDC equivalent to chrM: + egrep chrM * +# ucscToRefSeq.bed:chrM 0 16775 NC_001323.1 + # lookup that accession at NCBI Entrez: X52392.1 + # and add to ucscToINSDC.bed: + printf "chrM\t0\t16775\tX52392.1\n" >> ucscToINSDC.bed + # verify: + grep chrM * +# ucsc.genbank.tab:chrM X52392.1 +# ucsc.refseq.tab:chrM NC_001323.1 +# ucscToINSDC.bed:chrM 0 16775 X52392.1 +# ucscToRefSeq.bed:chrM 0 16775 NC_001323.1 + + export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` + echo $chrSize + # 27 + # use the $chrSize in this sed + sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ + | hgLoadSqlTab regenCho1 ucscToINSDC stdin ucscToINSDC.bed + # should be the same for ucscToRefSeq: + export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1` + echo $chrSize + # 27 + sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ + | sed -e 's/INSDC/RefSeq/g;' \ + | hgLoadSqlTab regenCho1 ucscToRefSeq stdin ucscToRefSeq.bed + + # should be quiet for all OK + checkTableCoords regenCho1 + + # should cover %100 entirely: + featureBits -countGaps regenCho1 ucscToINSDC + # 1065365425 bases of 1065365425 (100.000%) in intersection + featureBits -countGaps regenCho1 ucscToRefSeq + # 1065365425 bases of 1065365425 (100.000%) in intersection + +######################################################################### +# add chromAlias table (TBD - 2019-11-25 - Hiram) + + mkdir /hive/data/genomes/regenCho1/bed/chromAlias + cd /hive/data/genomes/regenCho1/bed/chromAlias + + ln -s ../../ucsc/ucsc.regeneron.name.translate regen.tab + ~/kent/src/hg/utils/automation/chromAlias.pl regen.tab \ + > regenCho1.chromAlias.tab + + join regen.tab <(sort -k1,1 ../../chrom.sizes) \ + | awk '{printf "%s\t0\t%d\t%s\n", $1, $3, $2}' > regen.alias.bed + + wc -l * +# 6846 regen.alias.bed +# 6846 regen.tab +# 6846 regenCho1.chromAlias.tab + + hgLoadSqlTab regenCho1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ + regenCho1.chromAlias.tab + + # display the Regeneron AGP file as a track: + + ln -s ../../ucsc/ucsc.agp ./translatedRegen.agp + + grep -v "^#" translatedRegen.agp | grep -w scaffold \ + | awk '{printf "%s\t%d\t%d\tgap\t0\t.\n", $1, $2-1, $3}' > regen.gaps.bed + + grep -v "^#" translatedRegen.agp | grep -v -w scaffold \ + | awk '{printf "%s\t%d\t%d\t%s\t0\t%s\n", $1, $2-1, $3, $6, $9}' \ + > regen.contigs.bed + + sort -k1,1 -k2,2n regen.gaps.bed regen.contigs.bed > regen.agp.bed + + hgLoadBed regenCho1 regenAGP regen.agp.bed + # Read 17962 elements of size 6 from regen.agp.bed + + cut -f1-4 regen.gaps.bed | hgLoadBed regenCho1 regenAGPGap stdin + # Read 5558 elements of size 4 from stdin + +######################################################################### +# fixup search rule for assembly track/gold table (DONE - 2019-11-25 - Hiram) + cd ~/kent/src/hg/makeDb/trackDb/criGri/regenCho1 + # preview prefixes and suffixes: + hgsql -N -e "select frag from gold;" regenCho1 \ + | sed -e 's/[0-9_FR]\+//;' | sort | uniq -c + 1 chrM + 7659 pi + 33 pisub + 3 pisuba + 3 pisubb + 51824 ss + + + # implies a rule: '[cps][his](sub)?[rM0-9]+(_[ab0-9FR]+)?' + + # verify this rule will find them all and eliminate them all: + hgsql -N -e "select frag from gold;" regenCho1 | wc -l + # 59523 + + hgsql -N -e "select frag from gold;" regenCho1 \ + | egrep -e '[cps][his]+(sub)?[rM0-9]+(_[ab0-9FR]+)?' | wc -l + # 59523 + + hgsql -N -e "select frag from gold;" regenCho1 \ + | egrep -v -e '[cps][his]+(sub)?[rM0-9]+(_[ab0-9FR]+)?' | wc -l + # 0 + + # hence, add to trackDb/chicken/regenCho1/trackDb.ra +searchTable gold +shortCircuit 1 +termRegex [cps][his]+(sub)?[rM0-9]+(_[ab0-9FR]+)? +query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' +searchPriority 8 + + # verify searches work in the position box + +########################################################################## +# running repeat masker (DONE - 2019-11-25 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/repeatMasker + cd /hive/data/genomes/regenCho1/bed/repeatMasker + time (doRepeatMasker.pl -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -smallClusterHub=ku regenCho1) > do.log 2>&1 & +XXX - running - Mon Nov 25 15:35:50 PST 2019 + # real 48m25.181s + + cat faSize.rmsk.txt +#2762428432 bases (227617579 N's 2534810853 real 1422483022 upper +# 1112327831 lower) in 6846 sequences in 1 files +#Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F) +# max 248247500 (ss100001) median 10668 +# %40.27 masked total, %43.88 masked real + + egrep -i "versi|relea" do.log +# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ +# February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker +# grep RELEASE /hive/data/staging/data/RepeatMasker/Libraries/RepeatMaskerLib.embl +# CC Dfam_Consensus RELEASE 20181026; * + + time featureBits -countGaps regenCho1 rmsk + # 1112341443 bases of 2762428432 (40.267%) in intersection + # real 0m35.822s + + # why is it different than the faSize above ? + # because rmsk masks out some N's as well as bases, the faSize count above + # separates out the N's from the bases, it doesn't show lower case N's + + # faster way to get the same result on high contig count assemblies: + time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' regenCho1 \ + | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" + # total 1112341443.000000 + # real 0m20.990s + +########################################################################## +# running simple repeat (DONE - 2019-11-25 - Hiram) + + # The '-trf409 4' is a bit smaller than human which is 6 + + mkdir /hive/data/genomes/regenCho1/bed/simpleRepeat + cd /hive/data/genomes/regenCho1/bed/simpleRepeat + time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ + -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ + -trf409=4 regenCho1) > do.log 2>&1 & +XXX - running - Mon Nov 25 15:36:08 PST 2019 + # real 58m3.288s + + cat fb.simpleRepeat + # 91165405 bases of 2534810853 (3.597%) in intersection + + cd /hive/data/genomes/regenCho1 + # when using the Window Masker result: + cd /hive/data/genomes/regenCho1 +# twoBitMask bed/windowMasker/regenCho1.cleanWMSdust.2bit \ +# -add bed/simpleRepeat/trfMask.bed regenCho1.2bit + # you can safely ignore the warning about fields >= 13 + + # or using the rmsk result after it is done: + twoBitMask regenCho1.rmsk.2bit \ + -add bed/simpleRepeat/trfMask.bed regenCho1.2bit + # you can safely ignore the warning about fields >= 13 + twoBitToFa regenCho1.2bit stdout | faSize stdin > faSize.regenCho1.2bit.txt + cat faSize.regenCho1.2bit.txt +# 2762428432 bases (227617579 N's 2534810853 real 1418746093 upper +# 1116064760 lower) in 6846 sequences in 1 files +# Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F) +# max 248247500 (ss100001) median 10668 +# %40.40 masked total, %44.03 masked real + + rm /gbdb/regenCho1/regenCho1.2bit + ln -s `pwd`/regenCho1.2bit /gbdb/regenCho1/regenCho1.2bit + +######################################################################### +# CREATE MICROSAT TRACK (TBD - 2019-06-29 - Hiram) + ssh hgwdev + mkdir /cluster/data/regenCho1/bed/microsat + cd /cluster/data/regenCho1/bed/microsat + + awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \ + ../simpleRepeat/simpleRepeat.bed > microsat.bed + + hgLoadBed regenCho1 microsat microsat.bed + # Read 228853 elements of size 4 from microsat.bed + +########################################################################## +## WINDOWMASKER (TBD - 2019-11-25 - Hiram) + # wait for RepeatMasker to finish before this, since this is going + # to compare itself with the rmsk result + + mkdir /hive/data/genomes/regenCho1/bed/windowMasker + cd /hive/data/genomes/regenCho1/bed/windowMasker + time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ + -dbHost=hgwdev regenCho1) > do.log 2>&1 + # real 26m58.753s + + # Masking statistics + cat faSize.regenCho1.cleanWMSdust.txt +# 2762428432 bases (227617579 N's 2534810853 real 1629368138 upper +# 905442715 lower) in 6846 sequences in 1 files +# Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F) +# max 248247500 (ss100001) median 10668 +# %32.78 masked total, %35.72 masked real + + cat fb.regenCho1.rmsk.windowmaskerSdust.txt + # 696560115 bases of 2762428432 (25.215%) in intersection + +########################################################################## +# cpgIslands - (TBD - 2019-06-29 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/cpgIslands + cd /hive/data/genomes/regenCho1/bed/cpgIslands + time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev -smallClusterHub=ku regenCho1) > do.log 2>&1 + # real 3m59.256s + + cat fb.regenCho1.cpgIslandExt.txt + # 10317331 bases of 2534810853 (0.407%) in intersection + +############################################################################## +# genscan - (TBD - 2019-06-29 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/genscan + cd /hive/data/genomes/regenCho1/bed/genscan + time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ + -bigClusterHub=ku regenCho1) > do.log 2>&1 + # real 126m0.077s + + cat fb.regenCho1.genscan.txt + # 54712419 bases of 2534810853 (2.158%) in intersection + + cat fb.regenCho1.genscanSubopt.txt + # 56830306 bases of 2534810853 (2.242%) in intersection + +######################################################################### +# Create kluster run files (TBD - 2019-06-29 - Hiram) + + # numerator is regenCho1 gapless bases "real" as reported by: + featureBits -noRandom -noHap regenCho1 gap + # 227617579 bases of 2534810853 (8.980%) in intersection + # ^^^ + # denominator is hg19 gapless bases as reported by: + # featureBits -noRandom -noHap hg19 gap + # 234344806 bases of 2861349177 (8.190%) in intersection + # 1024 is threshold used for human -repMatch: + calc \( 2534810853 / 2861349177 \) \* 1024 + # ( 2534810853 / 2861349177 ) * 1024 = 907.140706 + + # ==> use -repMatch=350 according to size scaled down from 1024 for human. + # and rounded down to nearest 50 + cd /hive/data/genomes/regenCho1 + blat regenCho1.2bit \ + /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/regenCho1.11.ooc \ + -repMatch=900 + # Wrote 29409 overused 11-mers to jkStuff/regenCho1.11.ooc + # rn6 was repMatch 1000 and: + # Wrote 27021 overused 11-mers to jkStuff/rn6.11.ooc + # rn5 at repMatch 950: Wrote 34513 overused 11-mers to jkStuff/rn5.11.ooc + + + # check non-bridged gaps to see what the typical size is: + hgsql -N \ + -e 'select * from gap where bridge="no" order by size;' regenCho1 \ + | sort -k7,7nr | ave -col=7 stdin + # min 51690.000000 + # max 136961.000000 + + gapToLift -verbose=2 -minGap=50000 regenCho1 jkStuff/nonBridged.lift \ + -bedFile=jkStuff/nonBridged.bed + wc -l jkStuff/nonBri* + # 6866 jkStuff/nonBridged.bed + # 6866 jkStuff/nonBridged.lift + +######################################################################## +# lastz/chain/net swap human/hg38 (TBD - 2019-11-25 - Hiram) + # original alignment + cd /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-25 + + cat fb.hg38.chainRegenCho1Link.txt + # 154079940 bases of 3095998939 (4.977%) in intersection + cat fb.hg38.chainSynRegenCho1Link.txt + # 95877644 bases of 3095998939 (3.097%) in intersection + cat fb.hg38.chainRBest.RegenCho1.txt + # 106665747 bases of 3095998939 (3.445%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/regenCho1/bed/blastz.hg38.swap + cd /hive/data/genomes/regenCho1/bed/blastz.hg38.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg38/bed/lastzRegenCho1.2019-11-25/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=loose \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 + # real 9m45.514s + + cat fb.regenCho1.chainHg38Link.txt + # 120955955 bases of 1055588482 (11.459%) in intersection + + cat fb.regenCho1.chainSynHg38Link.txt + # 92597630 bases of 1055588482 (8.772%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenCho1 hg38) > rbest.log 2>&1 & + # real 139m24.408s + + cat fb.regenCho1.chainRBest.Hg38.txt + # 106294585 bases of 1055588482 (10.070%) in intersection + +######################################################################### +# lastz/chain/net swap mouse/mm10 (TBD - 2019-11-25 - Hiram) + + # original alignment + cd /hive/data/genomes/mm10/bed/lastzRegenCho1.2019-11-25 + cat fb.mm10.chainRegenCho1Link.txt + # 101151132 bases of 2652783500 (3.813%) in intersection + cat fb.mm10.chainSynRegenCho1Link.txt + # 70707720 bases of 2652783500 (2.665%) in intersection + cat fb.mm10.chainRBest.RegenCho1.txt + # 79649474 bases of 2652783500 (3.002%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/regenCho1/bed/blastz.mm10.swap + cd /hive/data/genomes/regenCho1/bed/blastz.mm10.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzRegenCho1.2019-11-25/DEF \ + -swap -chainMinScore=5000 -chainLinearGap=loose \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 + # real 6m41.043s + + cat fb.regenCho1.chainMm10Link.txt + # 88539346 bases of 1055588482 (8.388%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenCho1 mm10) > rbest.log 2>&1 & + # real 94m11.007s + + cat fb.regenCho1.chainRBest.Mm10.txt + # 79474812 bases of 1055588482 (7.529%) in intersection + +######################################################################### +# GENBANK AUTO UPDATE (TBD - 2019-06-29 - Hiram) + ssh hgwdev + cd $HOME/kent/src/hg/makeDb/genbank + git pull + # /cluster/data/genbank/data/organism.lst shows: + # #organism mrnaCnt estCnt refSeqCnt + # Rattus norvegicus 130197 1103594 17642 + + # edit etc/genbank.conf to add regenCho1 just before galGal5 + +# regenCho1 (Regeneron rat assembly) +regenCho1.serverGenome = /hive/data/genomes/regenCho1/regenCho1.2bit +regenCho1.ooc = /hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc +regenCho1.lift = /hive/data/genomes/regenCho1/jkStuff/nonBridged.lift +regenCho1.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} +regenCho1.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} +regenCho1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} +regenCho1.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} +regenCho1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} +regenCho1.downloadDir = regenCho1 +regenCho1.refseq.mrna.xeno.load = yes +regenCho1.refseq.mrna.xeno.loadDesc = yes +regenCho1.genbank.mrna.xeno.load = yes +regenCho1.perChromTables = no +regenCho1.mgc = yes +# regenCho1.upstreamGeneTbl = ensGene +# regenCho1.upstreamMaf = multiz13way /hive/data/genomes/regenCho1/bed/multiz13way/species.list.txt + + # verify the files specified exist before checking in the file: + grep ^regenCho1 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og +# -rw-rw-r-- 1 247657 Jun 29 17:16 /hive/data/genomes/regenCho1/jkStuff/nonBridged.lift +# -rw-rw-r-- 1 117644 Jun 29 17:13 /hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc +# -rw-rw-r-- 1 720490674 Jun 29 16:59 /hive/data/genomes/regenCho1/regenCho1.2bit + + git commit -m "Added regenCho1 - Regeneron rat refs #21579" etc/genbank.conf + git push + # update /cluster/data/genbank/: + make etc-update + + # enable daily alignment and update of hgwdev + cd ~/kent/src/hg/makeDb/genbank + git pull + # add regenCho1 to: + # etc/align.dbs etc/hgwdev.dbs + git add etc/align.dbs etc/hgwdev.dbs + git commit -m "Added regenCho1 - Regeneron rat refs #21579" etc/hgwdev.dbs + git push + make etc-update + + # wait a few days for genbank magic to take place, the tracks will + # appear + +############################################################################# +# augustus gene track (TBD - 2019-06-29 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/augustus + cd /hive/data/genomes/regenCho1/bed/augustus + time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ + -species=human -dbHost=hgwdev \ + -workhorse=hgwdev regenCho1) > do.log 2>&1 + # real 194m56.414s + + cat fb.regenCho1.augustusGene.txt + # 48867584 bases of 2534810853 (1.928%) in intersection + +######################################################################### +# ncbiRefSeq (TBD - 2019-11-25 - Hiram) + + mkdir /hive/data/genomes/regenCho1/bed/ncbiRefSeq + cd /hive/data/genomes/regenCho1/bed/ncbiRefSeq + # running step wise just to be careful + time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev \ + -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ + refseq vertebrate_other Gallus_gallus \ + GCF_000002315.5_GRCg6a regenCho1) > download.log 2>&1 + # real 1m19.029s + + time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ + -continue=process -bigClusterHub=ku -dbHost=hgwdev \ + -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ + refseq vertebrate_other Gallus_gallus \ + GCF_000002315.5_GRCg6a regenCho1) > process.log 2>&1 + # real 2m6.030s + + time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ + -continue=load -bigClusterHub=ku -dbHost=hgwdev \ + -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ + refseq vertebrate_other Gallus_gallus \ + GCF_000002315.5_GRCg6a regenCho1) > load.log 2>&1 + # real 0m22.312s + + cat fb.ncbiRefSeq.regenCho1.txt + # 88641893 bases of 1055588482 (8.397%) in intersection + + # need to add: include ../../refSeqComposite.ra alpha + # to the chicken/regenCho1/trackDb.ra to turn on the track in the browser + + # there was one gene that claimed to have a protein, but the + # protein sequence was not included in the protein.faa file + # discovered from joinerCheck + # manual fix to blank out this one protein, to see the entry + hgsql -e 'select * from ncbiRefSeqLink where protAcc="NP_989875.1";' regenCho1 + hgsql -e 'update ncbiRefSeqLink set protAcc="" where protAcc="NP_989875.1";' regenCho1 + # this makes the 'protein' link disappear from the gene details page + # curious that this gene is marked as a non-coding gene anyway ? + # gene: FET1 at chr4:63,102,774-63,105,516- + + featureBits -enrichment regenCho1 refGene ncbiRefSeq + # refGene 1.374%, ncbiRefSeq 8.397%, both 1.370%, cover 99.73%, enrich 11.88x + featureBits -enrichment regenCho1 ncbiRefSeq refGene + # ncbiRefSeq 8.397%, refGene 1.374%, both 1.370%, cover 16.32%, enrich 11.88x + + featureBits -enrichment regenCho1 ncbiRefSeqCurated refGene + # ncbiRefSeqCurated 1.368%, refGene 1.374%, both 1.364%, cover 99.71%, enrich 72.59x + featureBits -enrichment regenCho1 refGene ncbiRefSeqCurated + # refGene 1.374%, ncbiRefSeqCurated 1.368%, both 1.364%, cover 99.32%, enrich 72.59x + +######################################################################### +# LIFTOVER TO rn6 (TBD - 2019-06-29 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/regenCho1/bed/blat.rn6.2019-06-29 + cd /hive/data/genomes/regenCho1/bed/blat.rn6.2019-06-29 + doSameSpeciesLiftOver.pl -verbose=2 \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -ooc=/hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc \ + regenCho1 rn6 + time (doSameSpeciesLiftOver.pl -verbose=2 \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -ooc=/hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc \ + regenCho1 rn6) > doLiftOverToRn6.log 2>&1 + # about 3 hours 20 minutes + + # see if the liftOver menus function in the browser from regenCho1 to galGal5 + + # would like to see this as a track: + time chainToPsl regenCho1ToRn6.over.chain.gz ../../chrom.sizes \ + /hive/data/genomes/rn6/chrom.sizes ../../regenCho1.2bit \ + /hive/data/genomes/rn6/regenCho1.2bit regenCho1ToRn6.psl +XXX - running - Mon Jul 1 13:33:33 PDT 2019 + +######################################################################### +# LIFTOVER TO regenRn1 (TBD - 2019-09-09 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/regenCho1/bed/blat.regenRn1.2019-09-09 + cd /hive/data/genomes/regenCho1/bed/blat.regenRn1.2019-09-09 + doSameSpeciesLiftOver.pl -verbose=2 \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -ooc=/hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc \ + regenCho1 regenRn1 + time (doSameSpeciesLiftOver.pl -verbose=2 \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -ooc=/hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc \ + regenCho1 regenRn1) > doLiftOverToRegenRn1.log 2>&1 + # real 248m28.261s + + # see if the liftOver menus function in the browser from regenCho1 to regenRn1 + + # would like to see this as a track: + hgLoadChain regenCho1 chainRegenRn1 regenCho1ToRegenRn1.over.chain.gz + # Loading 71615 chains into regenCho1.chainRegenRn1 + + chainSort regenCho1ToRegenRn1.over.chain.gz stdout \ + | chainPreNet stdin \ + /hive/data/genomes/regenCho1/chrom.sizes \ + /hive/data/genomes/regenRn1/chrom.sizes stdout \ + | chainNet stdin -minSpace=1 /hive/data/genomes/regenCho1/chrom.sizes \ + /hive/data/genomes/regenRn1/chrom.sizes stdout /dev/null \ + | netSyntenic stdin noClass.net + + netClass -verbose=0 -noAr noClass.net regenCho1 regenRn1 regenCho1.regenRn1.net + + netFilter -minGap=10 regenCho1.regenRn1.net \ + | hgLoadNet -verbose=0 regenCho1 netRegenRn1 stdin + + featureBits regenCho1 chainRegenRn1Link > fb.regenCho1.chainRegenRn1Link.txt 2>&1 + + cat fb.regenCho1.chainRegenRn1Link.txt + # 2436426341 bases of 2534810853 (96.119%) in intersection + +######################################################################### +# BLATSERVERS ENTRY (TBD - 2019-11-25 - Hiram) +# After getting a blat server assigned by the Blat Server Gods, + ssh hgwdev + + hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ + VALUES ("regenCho1", "blat1a", "17892", "1", "0"); \ + INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ + VALUES ("regenCho1", "blat1a", "17893", "0", "1");' \ + hgcentraltest + # test it with some sequence + +############################################################################ +## reset default position to MEPE gene (egg shell protein) +## (TBD - 2019-11-25 - Hiram) + + # as found from the galGal5 to regenCho1 liftOver + ssh hgwdev + hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928" + where name="regenCho1";' hgcentraltest + +######################################################################### +# crispr whole genome (WORKING - 2019-07-02 - Hiram) + mkdir /hive/data/genomes/regenCho1/bed/crisprAll + cd /hive/data/genomes/regenCho1/bed/crisprAll + + # working on this script, adding the indexFa step: + time (~/kent/src/hg/utils/automation/doCrispr.pl \ + -stop=indexFa -buildDir=`pwd` -smallClusterHub=ku regenCho1 augustusGene) \ + > indexFa.log 2>&1 +XXX - running - Tue Jul 2 11:09:39 PDT 2019 + # real 23m26.694s + + # the large shoulder argument will cause the entire genome to be scanned +~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \ + hg19 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev-101 -bigClusterHub=ku \ + -workhorse=hgwdev + + + time (~/kent/src/hg/utils/automation/doCrispr.pl \ + -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \ + regenCho1 ncbiRefSeq) > guides.log 2>&1 + # real 2m50.758s + + # adding the /dev/shm/ setup rsync for the indexed Fa + # performed manually to work out the procedure + time (~/kent/src/hg/utils/automation/doCrispr.pl \ + -continue=specScores -stop=specScores -buildDir=`pwd` \ + -smallClusterHub=ku regenCho1 ncbiRefSeq) > specScores.log + + # had about half of ku for about half this time: +# Completed: 884922 of 884922 jobs +# CPU time in finished jobs: 35872791s 597879.85m 9964.66h 415.19d 1.138 y +# IO & Wait Time: 899261s 14987.69m 249.79h 10.41d 0.029 y +# Average job time: 42s 0.69m 0.01h 0.00d +# Longest finished job: 88s 1.47m 0.02h 0.00d +# Submission to last job: 48045s 800.75m 13.35h 0.56d + + + time find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab + # real 236m17.220s + wc -l specScores.tab + # 66451712 specScores.tab + + time (~/kent/src/hg/utils/automation/doCrispr.pl \ + -continue=effScores -stop=load \ + -buildDir=`pwd` -smallClusterHub=ku regenCho1 ncbiRefSeq) \ + > load.log + # real 307m41.143s + +######################################################################### +# all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram) +xyz + cd $HOME/kent/src/hg/makeDb/schema + # verify all the business is done for release + ~/kent/src/hg/utils/automation/verifyBrowser.pl regenCho1 + + # fixup all.joiner until this is a clean output + joinerCheck -database=regenCho1 -tableCoverage all.joiner + joinerCheck -database=regenCho1 -times all.joiner + joinerCheck -database=regenCho1 -keys all.joiner + + # when clean, check in: + git commit -m 'adding rules for regenCho1 refs #22113' all.joiner + git push + # run up a 'make alpha' in hg/hgTables to get this all.joiner file + # into the hgwdev/genome-test system + + cd /hive/data/genomes/regenCho1 + time (makeDownloads.pl regenCho1) > downloads.log 2>&1 + # real 10m7.605s + + # now ready for pushQ entry + mkdir /hive/data/genomes/regenCho1/pushQ + cd /hive/data/genomes/regenCho1/pushQ + time (makePushQSql.pl -redmineList regenCho1) > regenCho1.pushQ.sql 2> stderr.out + # real 9m58.779s + + # remove the extra chainNet files from the listings: + sed -i -e "/etNig1/d" redmine.regenCho1.file.list + sed -i -e "/asAcu1/d" redmine.regenCho1.file.list + sed -i -e "/etNig1/d" redmine.regenCho1.table.list + sed -i -e "/onAlb1/d" redmine.regenCho1.table.list + sed -i -e "/asAcu1/d" redmine.regenCho1.table.list + sed -i -e "/Stickleback/d" redmine.regenCho1.releaseLog.txt + sed -i -e "/Tetraodon/d" redmine.regenCho1.releaseLog.txt + sed -i -e "/sparrow/d" redmine.regenCho1.releaseLog.txt + # remove the tandemDups and gapOverlap from the file list: + sed -i -e "/tandemDups/d" redmine.regenCho1.table.list + sed -i -e "/Tandem Dups/d" redmine.regenCho1.releaseLog.txt + sed -i -e "/gapOverlap/d" redmine.regenCho1.table.list + sed -i -e "/Gap Overlaps/d" redmine.regenCho1.releaseLog.txt + # real 7m21.629s + + # check for errors in stderr.out, some are OK, e.g.: + # WARNING: hgwdev does not have /gbdb/regenCho1/wib/gc5Base.wib + # WARNING: hgwdev does not have /gbdb/regenCho1/wib/quality.wib + # WARNING: hgwdev does not have /gbdb/regenCho1/bbi/quality.bw + # WARNING: regenCho1 does not have seq + # WARNING: regenCho1 does not have extFile + + # add the path names to the listing files in the redmine issue + # in the three appropriate entry boxes: + +# /hive/data/genomes/regenCho1/pushQ/redmine.regenCho1.file.list +# /hive/data/genomes/regenCho1/pushQ/redmine.regenCho1.releaseLog.txt +# /hive/data/genomes/regenCho1/pushQ/redmine.regenCho1.table.list + +#########################################################################