360bab4f0495de7c98aa842d94aa6a6cde876324 hiram Wed Sep 2 17:32:14 2020 -0700 running up window masker refs #24074 diff --git src/hg/makeDb/doc/calJac4/initialBuild.txt src/hg/makeDb/doc/calJac4/initialBuild.txt new file mode 100644 index 0000000..b60e3e8 --- /dev/null +++ src/hg/makeDb/doc/calJac4/initialBuild.txt @@ -0,0 +1,1382 @@ +# for emacs: -*- mode: sh; -*- + +# This file describes browser build for the calJac4 +# GCF_009663435.1 + +# Can use existing photograph (otherwise find one before starting here) + +######################################################################### +# Initial steps, reuse existing photograph (DONE - 2020-09-01 - Hiram) + +# To start this initialBuild.txt document, from a previous assembly document: + +mkdir ~/kent/src/hg/makeDb/doc/calJac4 +cd ~/kent/src/hg/makeDb/doc/calJac4 + +sed -e 's/mm39/calJac4/g; s/Mm39/CalJac4/g; s/DONE/TBD/g;' \ + ../mm39/initialBuild.txt > initialBuild.txt + +mkdir -p /hive/data/genomes/calJac4/refseq +cd /hive/data/genomes/calJac4 + +# reuse existing photo from calJac3: +cp -p ../calJac3/photoReference.txt . + +cat photoReference.txt +photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Marmoset%20(Callithrix%20jacchus)&id=79119 +photoCreditName Photo courtesy of NHGRI press photos + +## download from NCBI +cd /hive/data/genomes/calJac4/refseq + +time rsync -L -a -P --stats \ +rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/663/435/GCF_009663435.1_Callithrix_jacchus_cj1700_1.1/ ./ +# sent 3,522 bytes received 5,637,592,146 bytes 59,032,415.37 bytes/sec +# total size is 5,636,202,618 speedup is 1.00 + +# real 1m34.674s + +# this information is from the top of +# calJac4/refseq/*_assembly_report.txt +# (aka: calJac4/refseq/GCF_009663435.1_Callithrix_jacchus_cj1700_1.1_assembly_report.txt + +# Assembly name: Callithrix_jacchus_cj1700_1.1 +# Organism name: Callithrix jacchus (white-tufted-ear marmoset) +# Infraspecific name: strain=cj1700 +# Sex: female +# Taxid: 9483 +# BioProject: PRJNA566173 +# Submitter: McDonnell Genome Institute at Washington University +# Date: 2020-05-22 +# Assembly type: haploid +# Release type: major +# Assembly level: Chromosome +# Genome representation: full +# WGS project: WJHW01 +# Reference guided assembly: GCA_000004665.1 +# Genome coverage: 40.0x +# GenBank assembly accession: GCA_009663435.2 +# RefSeq assembly accession: GCF_009663435.1 +# RefSeq assembly and GenBank assemblies identical: no +# +## Assembly-Units: +## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name +## GCA_009663445.2 GCF_009663445.1 Primary Assembly +## GCF_013177605.1 non-nuclear + +# check assembly size for later reference: + +faSize G*_1.1_genomic.fna.gz + +# 2897824427 bases (38007443 N's 2859816984 real 1774139275 upper +# 1085677709 lower) in 964 sequences in 1 files +# Total size: mean 3006041.9 sd 20298858.9 min 285 (NW_023264940.1) +# max 217961735 (NC_048383.1) median 42174 +# %37.47 masked total, %37.96 masked real + +# Survey types of gaps: + +zgrep -v "^#" *gaps.txt.gz | cut -f5 | sort | uniq -c | sed -e 's/^/# /;' +# 15 between_scaffolds +# 22 centromere +# 1 unknown +# 341 within_scaffold + +# And total size in gaps: +zgrep -v "^#" *gaps.txt.gz | awk '{print $3-$2+1}' | ave stdin \ + | sed -e 's/^/# /;' +# Q1 100.000000 +# median 24093.000000 +# Q3 55774.500000 +# average 100283.488127 +# min 13.000000 +# max 1000000.000000 +# count 379 +# total 38007442.000000 +# standard deviation 236845.788902 + + # survey the sequence to see if it has IUPAC characters: + time zgrep -v "^>" G*_1.1_genomic.fna.gz \ + | perl -ne '{print join("\n",split(//))}' \ + | sed -e '/^$/d' | sort | uniq -c | sort -rn | sed -e 's/^/# /;' +# 511573847 T +# 510890385 A +# 376024857 G +# 375650186 C +# 334954379 t +# 334153924 a +# 208296872 g +# 208272534 c +# 38007443 N + +# real 31m20.194s + +############################################################################# +# establish config.ra file (DONE - 2020-09-01 - Hiram) + cd /hive/data/genomes/calJac4 + ~/kent/src/hg/utils/automation/prepConfig.pl calJac4 mammal marmoset \ + refseq/*_assembly_report.txt > calJac4.config.ra + + # fix commonName: +commonName White-tufted-ear marmoset +to: +commonName Marmoset + # fix orderKey: +orderKey 23305 +to +orderKey 13093 + # fix bioSample: +ncbiBioSample notFound +to +ncbiBioSample SAMN12783337 + +# see also: https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN12783337 + + # compare with previous version to see if it is sane: + diff calJac4.config.ra ../calJac3/calJac3.config.ra + + # verify it really does look sane + cat calJac4.config.ra +# config parameters for makeGenomeDb.pl: +db calJac4 +clade mammal +genomeCladePriority 35 +scientificName Callithrix jacchus +commonName White-tufted-ear marmoset +assemblyDate May 2020 +assemblyLabel McDonnell Genome Institute at Washington University +assemblyShortLabel Callithrix_jacchus_cj1700_1.1 +orderKey 13083 +# mitochondrial sequence included in refseq release +# mitoAcc NC_025586.1 +mitoAcc none +fastaFiles /hive/data/genomes/calJac4/ucsc/*.fa.gz +agpFiles /hive/data/genomes/calJac4/ucsc/*.agp +# qualFiles none +dbDbSpeciesDir marmoset +photoCreditURL http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Marmoset%20(Callithrix%20jacchus)&id=79119 +photoCreditName Photo courtesy of NHGRI press photos +ncbiGenomeId 442 +ncbiAssemblyId 7157801 +ncbiAssemblyName Callithrix_jacchus_cj1700_1.1 +ncbiBioProject 566173 +ncbiBioSample SAMN12783337 +genBankAccessionID GCF_009663435.1 +taxId 9483 + +############################################################################# +# setup UCSC named files (DONE - 2020-09-01 - Hiram) + + mkdir /hive/data/genomes/calJac4/ucsc + cd /hive/data/genomes/calJac4/ucsc + + # check for duplicate sequences: + time faToTwoBit -noMask ../refseq/G*_1.1_genomic.fna.gz refseq.2bit + # real 0m39.757s + + twoBitDup refseq.2bit + # no output is a good result, otherwise, would have to eliminate duplicates + # the scripts creating the fasta here will be creating a refseq.2bit file + # to be removed later + + # compare gaps with what the gaps.gz file reported: + twoBitInfo -nBed refseq.2bit refseq.gap.bed + awk '{print $3-$2}' *.gap.bed | ave stdin | sed -e 's/^/# /;' +# Q1 70.000000 +# median 24007.000000 +# Q3 55774.500000 +# average 100019.586842 +# min 1.000000 +# max 1000000.000000 +# count 380 +# total 38007443.000000 +# standard deviation 236589.057301 + + # comparing with above, there is 1 gap here more, appears to be size 1 + # Check what the AGP says later on here. The gaps file defined: +# count 379 +# total 38007442.000000 + + time ~/kent/src/hg/utils/automation/ucscCompositeAgp.pl \ + ../refseq/G*_1.1_genomic.fna.gz \ + ../refseq/*_assembly_structure/Primary_Assembly +NC_048383.1 chr1 +NC_048384.1 chr2 +NC_048385.1 chr3 +NC_048386.1 chr4 +NC_048387.1 chr5 +NC_048388.1 chr6 +NC_048389.1 chr7 +NC_048390.1 chr8 +NC_048391.1 chr9 +NC_048392.1 chr10 +NC_048393.1 chr11 +NC_048394.1 chr12 +NC_048395.1 chr13 +NC_048396.1 chr14 +NC_048397.1 chr15 +NC_048398.1 chr16 +NC_048399.1 chr17 +NC_048400.1 chr18 +NC_048401.1 chr19 +NC_048402.1 chr20 +NC_048403.1 chr21 +NC_048404.1 chr22 +NC_048405.1 chrX +NC_048406.1 chrY + +real 10m48.905s + + time ~/kent/src/hg/utils/automation/unplacedWithChroms.pl \ + ../refseq/*_assembly_structure/Primary_Assembly + # processed 930 sequences into chrUn.fa.gz + # real 0m13.261s + + time ~/kent/src/hg/utils/automation/unlocalizedWithChroms.pl \ + ../refseq/*_assembly_structure/Primary_Assembly +# 11 +# 1 +# 13 +# 10 +# 9 +# 12 +# 14 +# processed 9 sequences into chr*_random.gz 7 files + +# real 0m0.552s + + # bash syntax here + mitoAcc=`grep "^# mitoAcc" ../calJac4.config.ra | awk '{print $NF}'` + printf "# mitoAcc %s\n" "$mitoAcc" +# mitoAcc NC_025586.1 + + zcat \ + ../refseq/*_assembly_structure/non-nuclear/assem*/AGP/chrMT.comp.agp.gz \ + | grep -v "^#" | sed -e "s/^$mitoAcc/chrM/;" > chrM.agp + + cat chrM.agp +# chrM 1 16499 1 O KM588314.1 1 16499 + + + printf ">chrM\n" > chrM.fa + twoBitToFa -noMask refseq.2bit:$mitoAcc stdout | grep -v "^>" >> chrM.fa + gzip chrM.fa + + faSize chrM.fa.gz +# 16499 bases (0 N's 16499 real 16499 upper 0 lower) in 1 sequences in 1 files + + # verify fasta and AGPs agree + time faToTwoBit *.fa.gz test.2bit + # real 0m47.608s + + cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail -4 + # All AGP and FASTA entries agree - both files are valid + + # and no sequence lost from orginal: + twoBitToFa test.2bit stdout | faSize stdin +# 2897824427 bases (38007443 N's 2859816984 real 2859816984 upper 0 lower) +# in 964 sequences in 1 files +# Total size: mean 3006041.9 sd 20298858.9 min 285 (chrUn_NW_023264940v1) +# max 217961735 (chr1) median 42174 + + # same numbers as above (except for upper/lower masking) +# 2897824427 bases (38007443 N's 2859816984 real 1774139275 upper +# 1085677709 lower) in 964 sequences in 1 files + + # See if the AGP files define all the gaps: + # categories of gaps: + awk '$5 == "N"' *.agp | cut -f7 | sort | uniq -c | sed -e 's/^/# /;' +# 22 centromere +# 15 contig +# 341 scaffold + # the gaps file defined: +# 15 between_scaffolds +# 22 centromere +# 1 unknown +# 341 within_scaffold + + awk '$5 == "N"' *.agp | awk '{print $3-$2+1}' | ave stdin \ + | sed -e 's/^/# /;' +# Q1 100.000000 +# median 24230.500000 +# Q3 55834.000000 +# average 100548.682540 +# min 13.000000 +# max 1000000.000000 +# count 378 +# total 38007402.000000 +# standard deviation 237103.349286 + + # the 2bit sequence has 2 more gaps and 41 more bases in gap: +# count 380 +# total 38007443.000000 + + # the gaps file defined 1 more gap at 40 bases: +# count 379 +# total 38007442.000000 +XXX - TBD - Wed Sep 2 07:44:09 PDT 2020 + + # survey gap types from gap file + # the gaps file defines 23 more gaps than the AGP files, + # the gaps file defines 13 more gaps but 54 less bases than the sequence + # note the 'unknown' types (== 23 gaps) + zgrep -v "^#" ../refseq/*gaps* | cut -f5,6 | sort | uniq -c \ + | sed -e 's/^/# /;' +# 15 between_scaffolds na +# 22 centromere na +# 1 unknown inferred_from_sequence +# 341 within_scaffold map + + # the single 'unknown' gap is the 40 base gap that is not in the AGP files + zgrep "unknown" ../refseq/*gaps* + # NC_048406.1 8006927 8006966 40 unknown inferred_from_sequence + + # survey of AGP types of gaps: + # beware, can also be type U in col 5, doesn't happen here: + awk '$5 == "U"' *.agp (no output) + awk '$5 == "N"' *.agp | awk '{print $7,$NF}' | sort | uniq -c \ + | sed -e 's/^/# /;' +# 22 centromere na +# 15 contig na +# 341 scaffold map + + # name equivalences in the assembly_report file: + grep -v "^#" \ + ../refseq/G*_1.1_assembly_report.txt \ + | awk '{printf "%s\t%s\n", $1,$5}' | sort > ncbi.assembly.genbank.equivalence + grep -v "^#" \ + ../refseq/G*_1.1_assembly_report.txt \ + | awk '{printf "%s\t%s\n", $1,$7}' | sort > ncbi.assembly.refseq.equivalence + join -t$'\t' ncbi.assembly.genbank.equivalence \ + ncbi.assembly.refseq.equivalence > ncbi.genbank.refseq.names + (the MT sequence has 'na' for genbank name) + + # no longer need these temporary 2bit files + rm test.2bit refseq.2bit refseq.gap.bed + +############################################################################# +# Initial database build (DONE - 2020-09-02 - Hiram) + + # verify sequence and AGP are OK: + cd /hive/data/genomes/calJac4 + time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \ + -stop=agp calJac4.config.ra) > agp.log 2>&1 + # real 2m16.607s + + # then finish it off: + time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \ + -fileServer=hgwdev -continue=db calJac4.config.ra) > db.log 2>&1 + # real 15m10.248s + + # check in the trackDb files created in TemporaryTrackDbCheckout/ + # and add calJac4 to trackDb/makefile refs #22271 + # fixing up the images reference to calJac4.jpg + + # temporary symlink until masked sequence is available + cd /hive/data/genomes/calJac4 + ln -s `pwd`/calJac4.unmasked.2bit /gbdb/calJac4/calJac4.2bit + +############################################################################# +# verify gap table vs NCBI gap file (TBD - 2020-07-27 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/gap + cd /hive/data/genomes/calJac4/bed/gap + + zgrep -v "^#" ../../refseq/G*_gaps.txt.gz \ + | awk '{printf "%s\t%d\t%d\t%s_%s\n", $1,$2-1,$3,$5,$6}' \ + | sort -k1,1 -k2,2n > refseq.gap.bed + + # type survey: + cut -f4 *.bed | sort | uniq -c | sed -e 's/^/# /;' +# 60 between_scaffolds_na +# 20 centromere_na +# 21 short_arm_na +# 42 telomere_na +# 4 unknown_inferred_from_sequence +# 19 unknown_unspecified +# 5 within_scaffold_align_genus +# 36 within_scaffold_map +# 96 within_scaffold_paired-ends +# 44 within_scaffold_unspecified + + # how much defined by NCBI: + awk '{print $3-$2}' *.bed | ave stdin | grep -w total + # total 73600614.000000 + + # how much in the gap table: + hgsql -e 'select * from gap;' calJac4 | awk '{print $4-$3}' \ + | ave stdin | grep -w total + # total 73598294.000000 + + # an extra 2320 bases marked in the gap file + # Compare to mm10: + hgsql -e 'select * from gap;' mm10 | awk '{print $4-$3}' \ + | ave stdin | sed -e 's/^/# /;' +# Q1 100.000000 +# median 838.000000 +# Q3 50000.000000 +# average 113665.609898 +# min 0.000000 +# max 2890000.000000 +# count 687 +# total 78088274.000000 +# standard deviation 485103.795880 + + hgsql -e 'select * from gap;' calJac4 | awk '{print $4-$3}' \ + | ave stdin | sed -e 's/^/# /;' +# Q1 1357.000000 +# median 50000.000000 +# Q3 100000.000000 +# average 226456.289231 +# min 0.000000 +# max 2890000.000000 +# count 325 +# total 73598294.000000 +# standard deviation 687212.981441 + + +############################################################################## +# cpgIslands on UNMASKED sequence (DONE - 2020-09-02 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/cpgIslandsUnmasked + cd /hive/data/genomes/calJac4/bed/cpgIslandsUnmasked + + time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \ + -tableName=cpgIslandExtUnmasked \ + -maskedSeq=/hive/data/genomes/calJac4/calJac4.unmasked.2bit \ + -workhorse=hgwdev -smallClusterHub=ku calJac4) > do.log 2>&1 +XXX - running - Wed Sep 2 10:08:50 PDT 2020 + # real 3m30.591s + + cat fb.calJac4.cpgIslandExtUnmasked.txt + # 56535294 bases of 2481941580 (2.278%) in intersection + +############################################################################# +# cytoBandIdeo - (DONE - 2020-09-02 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/cytoBand + cd /hive/data/genomes/calJac4/bed/cytoBand + makeCytoBandIdeo.csh calJac4 + +############################################################################# +# run up idKeys files for chromAlias/ncbiRefSeq (TBD - 2020-07-27 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/idKeys + cd /hive/data/genomes/calJac4/bed/idKeys + + time (doIdKeys.pl \ + -twoBit=/hive/data/genomes/calJac4/calJac4.unmasked.2bit \ + -buildDir=`pwd` calJac4) > do.log 2>&1 & +XXX - running - Wed Sep 2 10:09:29 PDT 2020 + # real 0m45.175s + + cat calJac4.keySignature.txt + # 804f78d880a5a7f049c472046b563601 + +############################################################################# +# gapOverlap (DONE - 2020-09-02 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/gapOverlap + cd /hive/data/genomes/calJac4/bed/gapOverlap + time (doGapOverlap.pl \ + -twoBit=/hive/data/genomes/calJac4/calJac4.unmasked.2bit calJac4 ) \ + > do.log 2>&1 & +XXX - running - Wed Sep 2 10:10:14 PDT 2020 + # real 1m49.446s + + # there is one only: + wc -l bed.tab + # 1 bed.tab + cut -f2- bed.tab +chr6 47663669 47714277 chr6:47663670-47714277 304 + 47663669 47714277 0 2 304,304 0,50304 + + cat fb.calJac4.gapOverlap.txt + # 608 bases of 2728222451 (0.000%) in intersection + +############################################################################# +# tandemDups (DONE - 2020-09-02 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/tandemDups + cd /hive/data/genomes/calJac4/bed/tandemDups + time (~/kent/src/hg/utils/automation/doTandemDup.pl \ + -twoBit=/hive/data/genomes/calJac4/calJac4.unmasked.2bit calJac4) \ + > do.log 2>&1 & +XXX - running - Wed Sep 2 10:10:14 PDT 2020 + # real 440m10.886s + + # one job in pairedEnds needs more memory: + time ./runOne 29 20000 chrY tmp/chrY.bed.gz + # real 28m57.353s + + # continuing + time (~/kent/src/hg/utils/automation/doTandemDup.pl \ + -continue=collapsePairedEnds \ + -twoBit=/hive/data/genomes/calJac4/calJac4.unmasked.2bit calJac4) \ + > collapsePairedEnds.log 2>&1 & + # real 3m23.138s + + cat fb.calJac4.tandemDups.txt + # 66584052 bases of 2728222451 (2.441%) in intersection + + bigBedInfo calJac4.tandemDups.bb | sed -e 's/^/# /;' +# version: 4 +# fieldCount: 13 +# hasHeaderExtension: yes +# isCompressed: yes +# isSwapped: 0 +# extraIndexCount: 0 +# itemCount: 858,983 +# primaryDataSize: 22,513,298 +# primaryIndexSize: 62,976 +# zoomLevels: 9 +# chromCount: 57 +# basesCovered: 1,408,031,925 +# meanDepth (of bases covered): 5.083425 +# minDepth: 1.000000 +# maxDepth: 240.000000 +# std of depth: 8.811752 + +######################################################################### +# ucscToINSDC and ucscToRefSeq table/track (DONE - 2020-09-01 - Hiram) + # construct idKeys for the genbank sequence + mkdir /hive/data/genomes/calJac4/refseq/idKeys + cd /hive/data/genomes/calJac4/refseq/idKeys + faToTwoBit ../G*_1.1_genomic.fna.gz calJac4.refseq.2bit + time (doIdKeys.pl -buildDir=`pwd` \ + -twoBit=`pwd`/calJac4.refseq.2bit refseqCalJac4) > do.log 2>&1 & + + sed -e 's/^/# /;' refseqCalJac4.keySignature.txt + # 01e329dd4e2641908a563b4ff1c8b648 + + mkdir /hive/data/genomes/calJac4/genbank + cd /hive/data/genomes/calJac4/genbank + + faToTwoBit \ +/hive/data/outside/ncbi/genomes/GCA/009/663/435/GCA_009663435.2_Callithrix_jacchus_cj1700_1.1/GCA_009663435.2_Callithrix_jacchus_cj1700_1.1_genomic.fna.gz \ + calJac4.genbank.2bit + + time (doIdKeys.pl -buildDir=`pwd` \ + -twoBit=`pwd`/calJac4.genbank.2bit genbankCalJac4) > do.log 2>&1 & +XXX - running - Wed Sep 2 09:23:10 PDT 2020 + # real 0m45.317s + + sed -e 's/^/# /;' genbankCalJac4.keySignature.txt + # 804f78d880a5a7f049c472046b563601 + + mkdir /hive/data/genomes/calJac4/bed/chromAlias + cd /hive/data/genomes/calJac4/bed/chromAlias + + join -t$'\t' ../idKeys/calJac4.idKeys.txt \ + ../../genbank/idKeys/genbankCalJac4.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 + + # should be same line counts throughout: + wc -l * ../../chrom.sizes + # 61 ucscToINSDC.bed + # 61 ../../chrom.sizes + + export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1` + echo $chrSize + # 22 + # use the $chrSize in this sed + sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \ + | hgLoadSqlTab calJac4 ucscToINSDC stdin ucscToINSDC.bed + + # should be quiet for all OK + checkTableCoords calJac4 + + # should cover %100 entirely: + featureBits -countGaps calJac4 ucscToINSDC + # 2728222451 bases of 2728222451 (100.000%) in intersection + +######################################################################### +# add chromAlias table (TBD - 2020-07-27 - Hiram) + + mkdir /hive/data/genomes/calJac4/bed/chromAlias + cd /hive/data/genomes/calJac4/bed/chromAlias + + grep -v "^#" ../../refseq/G*_1.1_assembly_report.txt \ + | awk '{printf "%s\t%s\n", $5,$1}' | sort > ncbi.assembly.txt + + hgsql -N -e 'select chrom,name from ucscToINSDC;' calJac4 \ + | sort -k1,1 > ucsc.genbank.tab + + join -t$'\t' -1 2 <(sort -k2,2 ucsc.genbank.tab) ncbi.assembly.txt + + # lookup the chrM sequence in the assembly to determine the RefSeq ID: + printf "chrM\tNC_005089.1\n" > ucsc.refseq.tab + + wc -l *.tab + # 61 ucsc.assembly.tab + # 61 ucsc.genbank.tab + # 1 ucsc.refseq.tab + + ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \ + > calJac4.chromAlias.tab +# working: assembly +# working: genbank + +for t in assembly genbank +do + c0=`cat ucsc.$t.tab | wc -l` + c1=`grep $t calJac4.chromAlias.tab | wc -l` + ok="OK" + if [ "$c0" -ne "$c1" ]; then + ok="ERROR" + fi + printf "# checking $t: $c0 =? $c1 $ok\n" +done +# checking assembly: 61 =? 61 OK +# checking genbank: 61 =? 61 OK + + # verify chrM is here properly: + grep chrM calJac4.chromAlias.tab +# AY172335.1 chrM genbank +# MT chrM assembly +# NC_005089.1 chrM refseq + + hgLoadSqlTab calJac4 chromAlias ~/kent/src/hg/lib/chromAlias.sql \ + calJac4.chromAlias.tab + +######################################################################### +# fixup search rule for assembly track/gold table (TBD - 2020-07-27 - Hiram) + cd ~/kent/src/hg/makeDb/trackDb/mouse/calJac4 + # preview prefixes and suffixes: + hgsql -N -e "select frag from gold;" calJac4 \ + | sed -e 's/[0-9.]\+//;' | sort | uniq -c | sed -e 's/^/# /;' +# 15228 AC +# 816 AEKQ +# 8 AEKR +# 1 AF +# 3876 AL +# 1 AY +# 844 BX +# 191 CAAA +# 135 CR +# 684 CT +# 63 CU +# 37 FO +# 3 FP +# 29 FQ +# 14 LO +# 249 LXEJ +# 30 MF +# 44 MG +# 18 MH +# 2 MN + + # implies a rule: '[ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?' + + # verify this rule will find them all and eliminate them all: + hgsql -N -e "select frag from gold;" calJac4 | wc -l + # 22273 + + hgsql -N -e "select frag from gold;" calJac4 \ + | egrep -e '[ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?' | wc -l + # 1795 + + hgsql -N -e "select frag from gold;" calJac4 \ + | egrep -v -e '[ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?' | wc -l + # 0 + + # hence, add to trackDb/rhesus/calJac4/trackDb.ra +searchTable gold +shortCircuit 1 +termRegex [ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)? +query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%' +searchPriority 8 + + # verify searches work in the position box + + git commit -m 'adding search rule for gold/assembly track refs #22271' \ + trackDb.ra + +########################################################################## +# running repeat masker (DONE - 2020-09-02 - Hiram) + # using new repeat masker version 4.1.0 + mkdir /hive/data/genomes/calJac4/bed/repeatMasker + cd /hive/data/genomes/calJac4/bed/repeatMasker + time (doRepeatMasker.pl -buildDir=`pwd` \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -smallClusterHub=hgwdev calJac4) > do.log 2>&1 +XXX - running - Wed Sep 2 10:11:32 PDT 2020 + # real 402m37.300s + + cat faSize.rmsk.txt +# 2897824427 bases (38007443 N's 2859816984 real 1455718019 upper +# 1404098965 lower) in 964 sequences in 1 files +# Total size: mean 3006041.9 sd 20298858.9 min 285 (chrUn_NW_023264940v1) +# max 217961735 (chr1) median 42174 +# %48.45 masked total, %49.10 masked real + + egrep -i "versi|relea" do.log +# RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ +# CC Dfam_Consensus RELEASE 20181026; * +# CC RepBase RELEASE 20181026; + + sed -e 's/^/# /;' versionInfo.txt +# The repeat files provided for this assembly were generated using RepeatMasker. +# Smit, AFA, Hubley, R & Green, P., +# RepeatMasker Open-4.0. +# 1996-2010 <http://www.repeatmasker.org>. +# +# VERSION: +# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ +# Search Engine: Crossmatch [ 1.090518 ] +# Master RepeatMasker Database: /hive/data/staging/data/RepeatMasker181121/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20181026-rb20181026 ) +# +# +# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $ +# CC Dfam_Consensus RELEASE 20181026; * +# CC RepBase RELEASE 20181026; * +# # RepeatMasker engine: -engine crossmatch -s +# # RepeatMasker library options: -species 'Callithrix jacchus' +# +# PARAMETERS: +# /hive/data/staging/data/RepeatMasker/RepeatMasker -engine crossmatch -s -align -species 'Callithrix jacchus' + + time featureBits -countGaps calJac4 rmsk + # 1404097506 bases of 2897824427 (48.454%) in intersection + # real 0m23.891s + + # 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;' calJac4 \ + | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total" + # total 1404097506.000000 + # real 0m21.422s + +########################################################################## +# running simple repeat (DONE - 2020-09-02 - Hiram) + + mkdir /hive/data/genomes/calJac4/bed/simpleRepeat + cd /hive/data/genomes/calJac4/bed/simpleRepeat + time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \ + -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \ + -trf409=6 calJac4) > do.log 2>&1 + # real 128m26.410s + + cat fb.simpleRepeat + # 106897704 bases of 2859817025 (3.738%) in intersection + +XXX - when WM finished - Wed Sep 2 17:30:02 PDT 2020 + + cd /hive/data/genomes/calJac4 + # if using the Window Masker result: + cd /hive/data/genomes/calJac4 +# twoBitMask bed/windowMasker/calJac4.cleanWMSdust.2bit \ +# -add bed/simpleRepeat/trfMask.bed calJac4.2bit + # you can safely ignore the warning about fields >= 13 + + # add to rmsk after it is done: + twoBitMask calJac4.rmsk.2bit \ + -add bed/simpleRepeat/trfMask.bed calJac4.2bit + # you can safely ignore the warning about fields >= 13 + twoBitToFa calJac4.2bit stdout | faSize stdin > faSize.calJac4.2bit.txt + cat faSize.calJac4.2bit.txt +# 2728222451 bases (73600668 N's 2654621783 real 1460027726 upper +# 1194594057 lower) in 61 sequences in 1 files +# Total size: mean 44724958.2 sd 64970951.3 min 1976 (chr4_JH584295v1_random) +# max 195154279 (chr1) median 182347 +# %43.79 masked total, %45.00 masked real + + + rm /gbdb/calJac4/calJac4.2bit + ln -s `pwd`/calJac4.2bit /gbdb/calJac4/calJac4.2bit + +######################################################################### +# CREATE MICROSAT TRACK (DONE - 2020-09-02 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/calJac4/bed/microsat + cd /hive/data/genomes/calJac4/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 calJac4 microsat microsat.bed + # Read 41788 elements of size 4 from microsat.bed + +########################################################################## +## WINDOWMASKER (DONE - 2020-09-02 - Hiram) + + mkdir /hive/data/genomes/calJac4/bed/windowMasker + cd /hive/data/genomes/calJac4/bed/windowMasker + time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ + -dbHost=hgwdev calJac4) > do.log 2>&1 +XXX - running - Wed Sep 2 17:31:19 PDT 2020 + # real 90m16.169s + + # Masking statistics + cat faSize.calJac4.cleanWMSdust.txt +# 2482000080 bases (58500 N's 2481941580 real 1630728232 upper 851213348 lower) +# in 2198 sequences in 1 files +# Total size: mean 1129208.4 sd 8542765.0 min 13084 (chrUn_JAAHUQ010000994v1) +# max 124992030 (chrX) median 43246 +# %34.30 masked total, %34.30 masked real + + # completed before rmsk was done, to finish: + featureBits -countGaps calJac4 rmsk windowmaskerSdust 2> fb.calJac4.rmsk.windowmaskerSdust.txt + cat fb.calJac4.rmsk.windowmaskerSdust.txt + # 753903955 bases of 2728222451 (27.634%) in intersection + + time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \ + -continue=cleanup -dbHost=hgwdev calJac4) > cleanup.log 2>&1 + # real 1m7.841s + +########################################################################## +# cpgIslands - (TBD - 2020-07-30 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/cpgIslands + cd /hive/data/genomes/calJac4/bed/cpgIslands + time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev -smallClusterHub=ku calJac4) > do.log 2>&1 + # real 3m28.053s + + cat fb.calJac4.cpgIslandExt.txt + # 10571422 bases of 2654624157 (0.398%) in intersection + +############################################################################## +# genscan - (TBD - 2020-07-30 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/genscan + cd /hive/data/genomes/calJac4/bed/genscan + time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ + -bigClusterHub=ku calJac4) > do.log 2>&1 + # real 8m19.775s + + # one job broken: +./runGsBig2M.csh chr10 000 gtf/000/chr10.gtf pep/000/chr10.pep subopt/000/chr10.bed + # real 34m35.712s + + # continuing + time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \ + -continue=makeBed -bigClusterHub=ku calJac4) > makeBed.log 2>&1 + # real 0m45.365s + + cat fb.calJac4.genscan.txt + # 55445747 bases of 2654624157 (2.089%) in intersection + + cat fb.calJac4.genscanSubopt.txt + # 57607700 bases of 2654624157 (2.170%) in intersection + +######################################################################### +# ncbiGene (WORKING - 2020-07-30 - Hiram) + + mkdir /hive/data/genomes/calJac4/bed/xenoRefGene + cd /hive/data/genomes/calJac4/bed/xenoRefGene + + time (~/kent/src/hg/utils/automation/doXenoRefGene.pl -buildDir=`pwd` \ + -bigClusterHub=ku -workhorse=hgwdev -dbHost=hgwdev calJac4) > do.log 2>&1 & + # real 67m18.015s + +######################################################################### +# Create kluster run files (TBD - 2020-07-30 - Hiram) + + # numerator is calJac4 gapless bases "real" as reported by: + featureBits -noRandom -noHap calJac4 gap + # 73490654 bases of 2649940489 (2.773%) 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 \( 2649940489 / 2861349177 \) \* 1024 + # ( 2649940489 / 2861349177 ) * 1024 = 948.342510 + + # ==> use -repMatch=900 according to size scaled down from 1024 for human. + # and rounded down to nearest 50 + cd /hive/data/genomes/calJac4 + time blat calJac4.2bit \ + /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/calJac4.11.ooc \ + -repMatch=900 + # Wrote 31807 overused 11-mers to jkStuff/calJac4.11.ooc + # real 0m23.024s + + # mm10 at repMatch=1000: + # Wrote 27208 overused 11-mers to jkStuff/mm10.11.ooc + # real 2m9.568s + + # survey sizes of non-bridged gaps: + hgsql -N -e 'select size from gap where bridge="no" order by size;' \ + calJac4 | sort | uniq -c | sort -k2,2n | sed -e 's/^/# /;' +# 1 8000 +# 21 10000 +# 2 30000 +# 43 50000 +# 3 60000 +# 1 61000 +# 2 63000 +# 1 66000 +# 1 71000 +# 1 81000 +# 42 100000 +# 1 140000 +# 1 174000 +# 1 300000 +# 1 350000 +# 1 500000 +# 20 2890000 + + # and survey the bridged gaps over 5,000 bases: + hgsql -N -e 'select size from gap where bridge="yes" and size > 4999;' \ + calJac4 | sort | uniq -c | sort -k2,2n | sed -e 's/^/# /;' +# 2 5000 +# 1 7000 +# 1 15000 +# 1 15500 +# 1 16000 +# 1 18000 +# 1 18500 +# 1 19208 +# 1 20000 +# 1 25500 +# 1 30000 +# 1 49000 +# 44 50000 +# 1 79000 +# 2 100000 +# 1 135500 +# 1 145000 +# 1 166000 +# 1 200000 +# 1 222000 +# 1 225000 +# 1 285000 +# 1 295000 +# 3 300000 +# 1 360000 +# 1 425000 +# 1 430000 +# 1 522000 + + # use gap size of 5000 to construct a lift file: + gapToLift -allowBridged -verbose=2 -minGap=5000 calJac4 \ + jkStuff/calJac4.5Kgaps.lft -bedFile=jkStuff/calJac4.5Kgaps.bed + wc -l jkStuff/calJac4.5Kgaps* + # 176 jkStuff/calJac4.5Kgaps.bed + # 176 jkStuff/calJac4.5Kgaps.lft + + # to see the gaps used: + bedInvert.pl chrom.sizes jkStuff/calJac4.5Kgaps.bed \ + | cut -f4 | sort -n | uniq -c | less + +######################################################################## +# lastz/chain/net swap human/hg38 (TBD - 2020-04-10 - Hiram) + + # original alignment + cd /hive/data/genomes/hg38/bed/lastzCalJac4.2020-04-02 + + cat fb.hg38.chainCalJac4Link.txt + # 1549397508 bases of 3110768607 (49.808%) in intersection + cat fb.hg38.chainSynCalJac4Link.txt + # 1488468205 bases of 3110768607 (47.849%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + hg38 calJac4) > rbest.log 2>&1 & + # real 310m32.196s + + cat fb.hg38.chainRBest.CalJac4.txt + # 1425406620 bases of 3110768607 (45.822%) in intersection + + # and for the swap: + mkdir /hive/data/genomes/calJac4/bed/blastz.hg38.swap + cd /hive/data/genomes/calJac4/bed/blastz.hg38.swap + + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/hg38/bed/lastzCalJac4.2020-04-02/DEF \ + -swap -chainMinScore=3000 -chainLinearGap=medium \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -syntenicNet) > swap.log 2>&1 + # real 99m10.990s + + cat fb.calJac4.chainHg38Link.txt + # 1493209286 bases of 2481941580 (60.163%) in intersection + cat fb.calJac4.chainSynHg38Link.txt + # 1448164376 bases of 2481941580 (58.348%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + calJac4 hg38) > rbest.log 2>&1 & + # real 257m59.713s + + cat fb.calJac4.chainRBest.Hg38.txt + # 1425296830 bases of 2481941580 (57.427%) in intersection + +########################################################################### +# lastz/chain/net swap mouse/mm10 (TBD - 2020-04-20 - Hiram) + + # original alignment + cat fb.mm10.chainCalJac4Link.txt + # 777883731 bases of 2652783500 (29.323%) in intersection + cat fb.mm10.chainSynCalJac4Link.txt + # 736602602 bases of 2652783500 (27.767%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev mm10 calJac4 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 219m16.168s + + cat fb.mm10.chainRBest.CalJac4.txt + # 741307883 bases of 2652783500 (27.945%) in intersection + + mkdir /hive/data/genomes/calJac4/bed/blastz.mm10.swap + cd /hive/data/genomes/calJac4/bed/blastz.mm10.swap + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm10/bed/lastzCalJac4.2020-04-02/DEF \ + -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & + # real 50m20.639s + + cat fb.calJac4.chainMm10Link.txt + # 772902855 bases of 2481941580 (31.141%) in intersection + cat fb.calJac4.chainSynMm10Link.txt + # 737924732 bases of 2481941580 (29.732%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev calJac4 mm10 \ + -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & + # real 173m38.016s + + cat fb.calJac4.chainRBest.Mm10.txt + # 740357755 bases of 2481941580 (29.830%) in intersection + +############################################################################## +# GENBANK AUTO UPDATE (TBD - 2020-07-30 - Hiram) + ssh hgwdev + cd $HOME/kent/src/hg/makeDb/genbank + git pull + # /cluster/data/genbank/data/organism.lst shows: + # organism mrnaCnt estCnt refSeqCnt + # Mus musculus 581990 4871398 37663 + # Mus musculus albula 4 0 0 + # Mus musculus bactrianus 4 0 0 + # Mus musculus brevirostris 2 0 0 + # Mus musculus castaneus 28 2 0 + # Mus musculus domesticus 1703 70 0 + # Mus musculus kobuvirus 2 0 0 + # Mus musculus molossinus 38 0 0 + # Mus musculus musculus 71 4 0 + # Mus musculus musculus x M. m. castaneus 1 0 0 + # Mus musculus papillomavirus type 1 10 0 0 + # Mus musculus picornavirus 3 0 0 + # Mus musculus wagneri 2 0 0 + + # edit etc/genbank.conf to add calJac4 just after mm10 + +# calJac4 - (house mouse - GCA_000001635.9 - GRCm39) +calJac4.serverGenome = /hive/data/genomes/calJac4/calJac4.2bit +calJac4.ooc = /hive/data/genomes/calJac4/jkStuff/calJac4.11.ooc +calJac4.lift = /hive/data/genomes/calJac4/jkStuff/calJac4.5Kgaps.lft +calJac4.refseq.mrna.native.pslCDnaFilter = ${finished.refseq.mrna.native.pslCDnaFilter} +calJac4.refseq.mrna.xeno.pslCDnaFilter = ${finished.refseq.mrna.xeno.pslCDnaFilter} +calJac4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter} +calJac4.genbank.mrna.xeno.pslCDnaFilter = ${finished.genbank.mrna.xeno.pslCDnaFilter} +calJac4.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter} +calJac4.downloadDir = calJac4 +calJac4.refseq.mrna.xeno.load = yes +calJac4.refseq.mrna.xeno.loadDesc = yes +calJac4.genbank.mrna.xeno.load = yes +calJac4.genbank.mrna.blatTargetDb = yes +calJac4.upstreamGeneTbl = refGene +# calJac4.mgc = yes +# calJac4.orfeome = yes +# calJac4.ccds.buildId = 21 +# calJac4.upstreamMaf = multiz60way /hive/data/genomes/calJac4/bed/multiz60way/species.list + + # verify the files specified exist before checking in the file: + grep ^calJac4 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og +# -rw-rw-r-- 1 127236 Jul 30 09:23 /hive/data/genomes/calJac4/jkStuff/calJac4.11.ooc +# -rw-rw-r-- 1 7714 Jul 30 09:50 /hive/data/genomes/calJac4/jkStuff/calJac4.5Kgaps.lft +# -rw-rw-r-- 1 714181470 Jul 30 09:03 /hive/data/genomes/calJac4/calJac4.2bit + + git commit -m "Added calJac4 mouse; refs #22271" 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 calJac4 to: + # etc/hgwdev.dbs etc/align.dbs + git commit -m "Added calJac4 - mouse refs #22271" etc/hgwdev.dbs etc/align.dbs + git push + make etc-update + + # wait a few days for genbank magic to take place, the tracks will + # appear + +############################################################################# +# augustus gene track (TBD - 2020-07-30 - Hiram) + + mkdir /hive/data/genomes/calJac4/bed/augustus + cd /hive/data/genomes/calJac4/bed/augustus + time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \ + -species=human -dbHost=hgwdev \ + -workhorse=hgwdev calJac4) > do.log 2>&1 + # real 119m8.866s + + cat fb.calJac4.augustusGene.txt + # 49120541 bases of 2654624157 (1.850%) in intersection + +######################################################################### +# ncbiRefSeq (TBD - 2019-11-20 - Hiram) + ### XXX ### Not available on GCA/genbank assemblies + + mkdir /hive/data/genomes/calJac4/bed/ncbiRefSeq + cd /hive/data/genomes/calJac4/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_mammalian Gorilla_gorilla \ + GCA_008122165.1_Kamilah_GGO_v0 calJac4) > download.log 2>&1 + # real 1m37.523s + + 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_mammalian Gorilla_gorilla \ + GCF_008122165.1_Kamilah_GGO_v0 calJac4) > process.log 2>&1 + # real 2m9.450s + + 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_mammalian Gorilla_gorilla \ + GCF_008122165.1_Kamilah_GGO_v0 calJac4) > load.log 2>&1 + # real 0m21.982s + + cat fb.ncbiRefSeq.calJac4.txt + # 74279781 bases of 2999027915 (2.477%) in intersection + + # add: include ../../refSeqComposite.ra alpha + # to the gorilla/calJac4/trackDb.ra to turn on the track in the browser + + # XXX 2019-11-20 - ready for this after genbank runs + + featureBits -enrichment calJac4 refGene ncbiRefSeq + # refGene 0.402%, ncbiRefSeq 3.148%, both 0.402%, cover 99.90%, enrich 31.73x + featureBits -enrichment calJac4 ncbiRefSeq refGene + # ncbiRefSeq 3.148%, refGene 0.402%, both 0.402%, cover 12.76%, enrich 31.73x + + featureBits -enrichment calJac4 ncbiRefSeqCurated refGene + # ncbiRefSeqCurated 0.401%, refGene 0.402%, both 0.400%, cover 99.66%, enrich 247.79x + + featureBits -enrichment calJac4 refGene ncbiRefSeqCurated + # refGene 0.402%, ncbiRefSeqCurated 0.401%, both 0.400%, cover 99.33%, enrich 247.79x + +############################################################################## +# LIFTOVER TO mm10 (TBD - 2020-07-30 - Hiram) + ssh hgwdev + mkdir /hive/data/genomes/calJac4/bed/blat.mm10.2020-07-30 + cd /hive/data/genomes/calJac4/bed/blat.mm10.2020-07-30 + doSameSpeciesLiftOver.pl -verbose=2 \ + -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -query2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -querySizes=/hive/data/genomes/mm10/chrom.sizes \ + -ooc=/hive/data/genomes/calJac4/jkStuff/calJac4.11.ooc \ + calJac4 mm10 + time (doSameSpeciesLiftOver.pl -verbose=2 \ + -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \ + -query2Bit=/hive/data/genomes/mm10/mm10.2bit \ + -querySizes=/hive/data/genomes/mm10/chrom.sizes \ + -ooc=/hive/data/genomes/calJac4/jkStuff/calJac4.11.ooc \ + calJac4 mm10) > doLiftOverToMm10.log 2>&1 + # real 257m18.898s + + # see if the liftOver menus function in the browser from calJac4 to mm10 + +############################################################################## +# BLATSERVERS ENTRY (TBD - 2020-04-02 - Hiram) +# request sent 2020-08-17 +# After getting a blat server assigned by the Blat Server Gods, + ssh hgwdev + + hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ + VALUES ("calJac4", "blat1b", "17904", "1", "0"); \ + INSERT INTO blatServers (db, host, port, isTrans, canPcr) \ + VALUES ("calJac4", "blat1b", "17905", "0", "1");' \ + hgcentraltest + # test it with some sequence + +############################################################################ +## reset default position to gene: CDH2 upon recommendation from Kerstin +## (TBD - 2020-06-22 - Hiram) + + ssh hgwdev + hgsql -e 'update dbDb set defaultPos="chr7:60683331-61003907" + where name="calJac4";' hgcentraltest + +############################################################################## +# crispr whole genome (TBD - 2020-07-30 - Hiram) + mkdir /hive/data/genomes/calJac4/bed/crisprAll + cd /hive/data/genomes/calJac4/bed/crisprAll + + # the large shoulder argument will cause the entire genome to be scanned + # this takes a while for a new genome to get the bwa indexing done + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \ + calJac4 augustusGene -shoulder=250000000 -tableName=crisprAll \ + -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) >> ranges.log 2>&1 + # real 62m2.060s - failed on 'genscan' genes + # real 1m16.884s - rerun on 'augustusGene' + + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ + -continue=guides -stop=specScores calJac4 augustusGene \ + -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) > specScores.log 2>&1 + # real 6558m26.295s + + cat guides/run.time | sed -e 's/^/# /;' +# Completed: 100 of 100 jobs +# CPU time in finished jobs: 13031s 217.19m 3.62h 0.15d 0.000 y +# IO & Wait Time: 299s 4.98m 0.08h 0.00d 0.000 y +# Average job time: 133s 2.22m 0.04h 0.00d +# Longest finished job: 920s 15.33m 0.26h 0.01d +# Submission to last job: 935s 15.58m 0.26h 0.01d + + cat specScores/run.time | sed -e 's/^/# /;' +# Completed: 2947790 of 2947790 jobs +# CPU time in finished jobs: 247411142s 4123519.03m 68725.32h 2863.55d 7.845 y +# IO & Wait Time: 0s 0.00m 0.00h 0.00d 0.000 y +# Average job time: 82s 1.37m 0.02h 0.00d +# Longest finished job: 353s 5.88m 0.10h 0.00d +# Submission to last job: 561467s 9357.78m 155.96h 6.50d + + +# Number of specScores: 220274834 + + ### remember to get back to hgwdev to run this + time (~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 \ + -continue=effScores -stop=load calJac4 augustusGene \ + -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \ + -buildDir=`pwd` -smallClusterHub=hgwdev -bigClusterHub=ku \ + -workhorse=hgwdev) > load.log 2>&1 + # real 1615m13.200s + + cat effScores/run.time | sed -e 's/^/# /;' +# Completed: 27714 of 27714 jobs +# CPU time in finished jobs: 13108172s 218469.53m 3641.16h 151.71d 0.416 y +# IO & Wait Time: 52457s 874.29m 14.57h 0.61d 0.002 y +# Average job time: 475s 7.91m 0.13h 0.01d +# Longest finished job: 2486s 41.43m 0.69h 0.03d +# Submission to last job: 44334s 738.90m 12.31h 0.51d + + cat offTargets/run.time | sed -e 's/^/# /;' +# Completed: 147390 of 147390 jobs +# CPU time in finished jobs: 2280286s 38004.77m 633.41h 26.39d 0.072 y +# IO & Wait Time: 505943s 8432.38m 140.54h 5.86d 0.016 y +# Average job time: 19s 0.32m 0.01h 0.00d +# Longest finished job: 36s 0.60m 0.01h 0.00d +# Submission to last job: 13489s 224.82m 3.75h 0.16d + + bigBedInfo crispr.bb | sed -e 's/^/# /;' +# version: 4 +# fieldCount: 22 +# hasHeaderExtension: yes +# isCompressed: yes +# isSwapped: 0 +# extraIndexCount: 0 +# itemCount: 276,331,386 +# primaryDataSize: 12,229,621,910 +# primaryIndexSize: 17,345,476 +# zoomLevels: 10 +# chromCount: 33 +# basesCovered: 2,179,930,088 +# meanDepth (of bases covered): 2.915516 +# minDepth: 1.000000 +# maxDepth: 32.000000 +# std of depth: 1.944181 + +######################################################################### +# all.joiner update, downloads and in pushQ - (WORKING - 2019-11-20 - Hiram) + cd $HOME/kent/src/hg/makeDb/schema + # verify all the business is done for release + ~/kent/src/hg/utils/automation/verifyBrowser.pl calJac4 +# 66 tables in database calJac4 - Dog, Canis lupus familiaris +# verified 55 tables in database calJac4, 11 extra tables, 14 optional tables +# chainNetRBestHg38 3 optional tables +# chainNetRBestMm10 3 optional tables +# chainNetSynHg38 3 optional tables +# chainNetSynMm10 3 optional tables +# gapOverlap 1 optional tables +# tandemDups 1 optional tables +# 1 chainCanFam3 - extra table +# 2 chainCanFam3Link - extra table +# 3 chainRBestCanFam3 - extra table +# 4 chainRBestCanFam3Link - extra table +# . . . etc . . . +# 8 crisprAllTargets - extra table +# 9 netCanFam3 - extra table +# 10 netRBestCanFam3 - extra table +# 11 netSynCanFam3 - extra table +# 13 genbank tables found +# verified 28 required tables, 1 missing tables +# 1 ucscToRefSeq - missing table +# hg38 chainNet to calJac4 found 3 required tables +# mm10 chainNet to calJac4 found 3 required tables +# hg38 chainNet RBest and syntenic to calJac4 found 6 optional tables +# mm10 chainNet RBest and syntenic to calJac4 found 3 optional tables +# liftOver to previous versions: 1, from previous versions: 1 + + # fixup all.joiner until this is a clean output + joinerCheck -database=calJac4 -tableCoverage all.joiner + joinerCheck -database=calJac4 -times all.joiner + joinerCheck -database=calJac4 -keys all.joiner + + # when clean, check in: + git commit -m 'adding rules for calJac4 refs #22271' all.joiner + git push + # run up a 'make alpha' in hg/hgTables to get this all.joiner file + # into the hgwdev/genome-test system + + cd /hive/data/genomes/calJac4 + time (makeDownloads.pl calJac4) > downloads.log 2>&1 + # real 16m11.233s + + # now ready for pushQ entry + mkdir /hive/data/genomes/calJac4/pushQ + cd /hive/data/genomes/calJac4/pushQ + time ($HOME/kent/src/hg/utils/automation/makePushQSql.pl -redmineList calJac4) > calJac4.pushQ.sql 2> stderr.out + # real 15m2.385s + + # remove the tandemDups and gapOverlap from the file list: + sed -i -e "/tandemDups/d" redmine.calJac4.table.list + sed -i -e "/Tandem Dups/d" redmine.calJac4.releaseLog.txt + sed -i -e "/gapOverlap/d" redmine.calJac4.table.list + sed -i -e "/Gap Overlaps/d" redmine.calJac4.releaseLog.txt + + # check for errors in stderr.out, some are OK, e.g.: + # WARNING: calJac4 does not have ucscToRefSeq + # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqVersion.txt + # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.bb + # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.ix + # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/ncbiRefSeqOther.ixx + # WARNING: hgwdev does not have /gbdb/calJac4/ncbiRefSeq/seqNcbiRefSeq.rna.fa + # WARNING: calJac4 does not have seq + # WARNING: calJac4 does not have extFile + + # verify the file list does correctly match to files + cat redmine.calJac4.file.list | while read L +do + eval ls $L > /dev/null +done + # should be silent, missing files will show as errors + + # verify database tables, how many to expect: + wc -l redmine.calJac4.table.list + # 52 redmine.calJac4.table.list + + # how many actual: + awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.calJac4.table.list | sh | wc -l + # 52 + + # would be a smaller number actual if some were missing + + # add the path names to the listing files in the redmine issue + # in the three appropriate entry boxes: + +# /hive/data/genomes/calJac4/pushQ/redmine.calJac4.file.list +# /hive/data/genomes/calJac4/pushQ/redmine.calJac4.releaseLog.txt +# /hive/data/genomes/calJac4/pushQ/redmine.calJac4.table.list + +#########################################################################