f5183290e802b44254b3b4d381f369cee8390fca markd Wed Apr 29 11:09:57 2020 -0700 moved gencode track doc to their own files for mm10 and hg19 as it is overwhelming the main file diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index 9cd4971..d3fa5a4 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -9919,77 +9919,30 @@ $aas = "$refRow->[2],$aas"; $codons = "$refRow->[3],$codons"; \ } \ $lineOut = "$lastCtg\t$lastS\t$lastE\trs$lastRs\t$lastTx\t$lastFrm\t" . \ "$count\t$fxns\t$nts\t$codons\t$aas\n"; \ $lineOut =~ s@NULL@n/a@g; \ print $lineOut;' \ ncbiCodingAnnotations.txt \ | liftUp snp138CodingDbSnp.bed suggested.lft warn stdin hgLoadBed mm10 snp138CodingDbSnp -sqlTable=$HOME/kent/src/hg/lib/snp125Coding.sql \ -renameSqlTable -tab -notItemRgb -allowStartEqualEnd \ snp138CodingDbSnp.bed #Read 1025678 elements of size 11 from snp138CodingDbSnp.bed ############################################################################## -2013-12-13: import of UCSC GENCODE group processing of GENCODE VM2 (markd) - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM2 - cd /hive/data/genomes/mm10/bed/gencodeVM2 - - # create Makefile from previous one. - cp /hive/data/genomes/hg19/bed/gencodeV19/Makefile . - - # download, build and load tables - (time nice make -j 10) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - # NOT DONE THIS TIME, SINCE THIS is the first mouse. - make cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. - ## Important to make sure filter attrs.transcriptType matches current set - ## figured out with - select distinct transcriptType from wgEncodeGencodeAttrsVM2 order by transcriptType; - cd kent/src/hg/makeDb/trackDb - cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM2.ra - cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM2.html - - # edit these plus human/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM2.ra in reverse order with previous - # tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous -0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers - ### track handler for this version of gencode: - registerTrackHandler("wgEncodeGencodeVM2", gencodeGeneMethods); - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - cd /hive/data/genomes/mm10/bed/gencodeVM2 - make joinerCheck - # see output in check/joiner.out -############################################################################## # SEGMENTAL DUPLICATIONS (WORKING 4/14/14 Pauline) # File emailed from John Huddleston (jlhudd@uw.edu) in the Eichler Lab. mkdir /hive/data/genomes/mm10/bed/genomicSuperDups cd /hive/data/genomes/mm10/bed/genomicSuperDups wget --timestamping 'http://mouseparalogy.gs.washington.edu/GRCm38/genomicSuperDup.tab' mv genomicSuperDup.tab mm10_WGAC.tab awk '($3 - $2) >= 1000 && ($9 - $8) >= 1000 {print;}' mm10_WGAC.tab \ | hgLoadBed mm10 genomicSuperDups stdin \ -tab -sqlTable=$HOME/kent/src/hg/lib/genomicSuperDups.sql # mm8 version of track had issue where strand values were "+" and "_" -- # checked and found same issue - so ran same fix: @@ -10620,85 +10573,30 @@ # 95837 # 42378 # 50621 # 100472 # 58582 # 28550 # 78772 # 83062 # 50849 # 324259 # 72540 # 11809 # 4269 ############################################################################## -# 2014-08-17: import of UCSC GENCODE group processing of GENCODE VM3 (markd) - - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM3/data - cd /hive/data/genomes/mm10/bed/gencodeVM3 - - # download gencode release - cd data - wget -nv -r -np ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3 - mv ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3 . - rm -rf ftp.sanger.ac.uk - - cd .. - # create Makefile from previous one. - cp /hive/data/genomes/mm10/bed/gencodeVM2/Makefile . - - # build and load tables - (time nice make -j 10) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. - ## Important to make sure filter attrs.transcriptType matches current set - ## figured out with - select distinct transcriptType from wgEncodeGencodeAttrsVM3 order by transcriptType; - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM3.ra - cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM3.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM3.ra in reverse order with previous - # tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers - ### track handler for this version of gencode: - registerTrackHandler("wgEncodeGencodeVM3", gencodeGeneMethods); - - # update all.joiner and validate - # look for the last section `begin Gencode VM?' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - cd /hive/data/genomes/mm10/bed/gencodeVM3 - make joinerCheck # output in check/joiner.out - -############################################################################## # LASTZ Cow bosTau8 (DONE - 2014-10-15 - Steve) mkdir /hive/data/genomes/mm10/bed/lastzBosTau8.2014-10-15 cd /hive/data/genomes/mm10/bed/lastzBosTau8.2014-10-15 cat << '_EOF_' > DEF # mouse vs cow # maximum M allowed with lastz is only 254 BLASTZ_M=254 # TARGET: Mouse mm10 SEQ1_DIR=/hive/data/genomes/mm10/nib SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=10000000 SEQ1_LAP=10000 @@ -10729,79 +10627,30 @@ mkdir /hive/data/genomes/bosTau8/bed/blastz.mm10.swap cd /hive/data/genomes/bosTau8/bed/blastz.mm10.swap time nice -n +19 doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzBosTau8.2014-10-15/DEF \ -swap -syntenicNet \ -noLoadChainSplit \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1 # real 58m4.272s cat fb.bosTau8.chainMm10Link.txt # 687270584 bases of 2649307237 (25.942%) in intersection # Create link cd /hive/data/genomes/bosTau8/bed ln -s blastz.mm10.swap lastz.mm10 -############################################################################ -# 2014-12-05: import of UCSC GENCODE group processing of GENCODE VM4 (markd) - - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM4/data - cd /hive/data/genomes/mm10/bed/gencodeVM4 - - # create Makefile from previous one. - # WARNING: next build start with hg/makeDb/outside/gencode/gencodeLoad.mk - cp /hive/data/genomes/hg38/bed/gencodeV21/Makefile . - - # download, build and load tables - (time nice make -j 10) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. - ## Important to make sure filter attrs.transcriptType matches current set - ## figured out with - select distinct transcriptType from wgEncodeGencodeAttrsVM4 order by transcriptType; - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM4.ra - cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM4.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM4.ra in reverse order with previous - # tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers - ### track handler for this version of gencode: - registerTrackHandler("wgEncodeGencodeVM4", gencodeGeneMethods); - - # update all.joiner and validate - # look for the last section `begin Gencode VM?' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - cd /hive/data/genomes/mm10/bed/gencodeVM4 - make joinerCheck # output in check/joiner.out - ############################################################################## ############################################################################## # TransMap V3 tracks. see makeDb/doc/transMapTracks.txt (2014-12-21 markd) ############################################################################## # LASTZ mouse/mm10 sheep/oviAri3 - (DONE - 2015-01-08 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzOviAri3.2015-01-08 cd /hive/data/genomes/mm10/bed/lastzOviAri3.2015-01-08 cp -p \ /hive/users/hiram/multiz/100way/mm10.oviAri3/mm10.oviAri3.tuning.top400.txt \ ./mm10.oviAri3.tuning.Q.txt cat << '_EOF_' > DEF # mouse vs sheep # parameters obtained from a tuning run of lastz_D @@ -11325,75 +11174,30 @@ http://genome.crg.es/genepredictions/M.musculus/mm10/SGP2/hg38/mm10.sgp2.gtf wget --timestamping \ http://genome.crg.es/genepredictions/M.musculus/mm10/SGP2/hg38/mm10.sgp2.gff3 ldHgGene -gtf -genePredExt mm10 sgpGene mm10.sgp2.gtf # Read 35235 transcripts in 287314 lines in 1 files # 35235 groups 60 seqs 1 sources 3 feature types # 35235 gene predictions featureBits -enrichment mm10 refGene:CDS sgpGene # refGene:CDS 1.292%, sgpGene 1.430%, both 1.101%, cover 85.21%, enrich 59.59x featureBits -enrichment mm9 refGene:CDS sgpGene # refGene:CDS 1.305%, sgpGene 1.439%, both 1.113%, cover 85.23%, enrich 59.23x ######################################################################### -2015-06-29-13: import of UCSC GENCODE group processing of GENCODE VM5 (markd) - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM5 - cd /hive/data/genomes/mm10/bed/gencodeVM5 - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set - # release and transcript support versions - - - # download, build and load tables - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. - ## Important to make sure filter attrs.transcriptType matches current set - ## figured out with - select distinct transcriptType from wgEncodeGencodeAttrsVM5 order by transcriptType; - cd kent/src/hg/makeDb/trackDb - cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM5.ra - cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM5.html - - # edit these plus human/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM5.ra in reverse order with previous - # tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM5 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - -######################################################################### # lastz zebrafish danRer10 (DONE - 2015-09-11 - Hiram) # establish a screen to control this job with a name to indicate what it is screen -S mm10DanRer10 mkdir /hive/data/genomes/mm10/bed/lastzDanRer10.2015-09-11 cd /hive/data/genomes/mm10/bed/lastzDanRer10.2015-09-11 cat << '_EOF_' > DEF # Mouse vs. zebrafish BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_Q=/scratch/data/blastz/HoxD55.q # TARGET: Mouse Mm10 @@ -11432,72 +11236,30 @@ mkdir /hive/data/genomes/danRer10/bed/blastz.mm10.swap cd /hive/data/genomes/danRer10/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzDanRer10.2015-09-11/DEF \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -swap -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 & # real 16m8.387s cat fb.danRer10.chainMm10Link.txt # 71611488 bases of 1369683683 (5.228%) in intersection time (doRecipBest.pl -buildDir=`pwd` danRer10 mm10) > rbest.log 2>&1 # real 7m34.259s ######################################################################### -2015-10-02: import of UCSC GENCODE group processing of GENCODE VM7 (markd) - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM7 - cd /hive/data/genomes/mm10/bed/gencodeVM7 - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set - # release and transcript support versions - - - # download, build and load tables - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructiuons in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM4.ra mouse/mm10/wgEncodeGencodeVM7.ra - cp mouse/mm10/wgEncodeGencodeVM4.html mouse/mm10/wgEncodeGencodeVM7.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM7.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM7 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - -######################################################################### # DBSNP 142 / SNP142 (DONE 2015-11-20 braney) # RedMine #15934 screen -S mm10dbSnp mkdir -p /hive/data/outside/dbSNP/142/mouse_mm10 cd /hive/data/outside/dbSNP/142/mouse_mm10 # Look at the directory listing of ftp://ftp.ncbi.nih.gov/snp/database/organism_data/ # to find the subdir name to use as orgDir below (mouse_10090 in this case). # Then click into that directory and look for file names like # b(1[0-9][0-9])_ # -- use the first num for build setting in config.ra # The buildAssembly setting in config.ra is empty because dbSNP stopped including # that in file names. cat > config.ra <<EOF db mm10 orgDir mouse_10090 @@ -11770,113 +11532,30 @@ # now join meta with bed file cd ../mm10 sort by name # The -S10G parameter is only supported in newer sort versions # # if it complains, just remove it. It will just take longer. time sort -k4,4 -S10G --parallel=20 mm10.bed > mm10.s4.bed join -t $'\t' -1 4 -2 1 ../data/mm10.s4.bed ../data/seqAndPatentSummary.tab -o '1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 2.10 2.11 2.12' | patSeqFilterBulkAndAnnotate ../data/htPatents.txt patBulk.bed patNonBulk.bed -c ../data/seqCounts.tab bedSort patNonBulk.bed patNonBulk.bed bedSort patBulk.bed patBulk.bed bedToBigBed patNonBulk.bed /cluster/data/genomes/mm10/chrom.sizes patNonBulk.bb -tab -as=../patSummary.as -type=bed12+ bedToBigBed patBulk.bed /cluster/data/genomes/mm10/chrom.sizes patBulk.bb -tab -as=../patSummary.as -type=bed12+ hgBbiDbLink hg19 patBulk /gbdb/hg19/bbi/patBulk.bb hgBbiDbLink hg19 patNonBulk /gbdb/hg19/bbi/patNonBulk.bb -######################################################################### -2016-03-14: import of UCSC GENCODE group processing of GENCODE VM8 (markd) -# not to be pushed to RR - - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM8 - cd /hive/data/genomes/mm10/bed/gencodeVM8 - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructions in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM7.ra mouse/mm10/wgEncodeGencodeVM8.ra - cp mouse/mm10/wgEncodeGencodeVM7.html mouse/mm10/wgEncodeGencodeVM8.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM8.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM8 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - -######################################################################### -2016-03-14: import of UCSC GENCODE group processing of GENCODE VM9 (markd) - - # download files - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM9 - cd /hive/data/genomes/mm10/bed/gencodeVM9 - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructions in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM9.ra - cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM9.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM9.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM9 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - ############################################################################## # LASTZ Rat rn6 (DONE - 2016-04-09 - Jonathan) mkdir /hive/data/genomes/mm10/bed/lastzRn6.2016-04-07 cd /hive/data/genomes/mm10/bed/lastzRn6.2016-04-07 printf '# rat vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rat Rn6 SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit @@ -12330,69 +12009,30 @@ time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzPanPan2.2016-05-24/DEF \ -swap -chainMinScore=3000 -chainLinearGap=medium \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 # real 106m54.032s cat fb.panPan2.chainMm10Link.txt # 911279510 bases of 2725937399 (33.430%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panPan2 mm10) \ > rbest.log 2>&1 # real 620m0.039s ######################################################################### -2016-07-22: import of UCSC GENCODE group processing of GENCODE VM10 (markd) - # will not be pushed to the RR. - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM10 - pushd /hive/data/genomes/mm10/bed/gencodeVM10 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. Results are in gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructions in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM9.ra mouse/mm10/wgEncodeGencodeVM10.ra - cp mouse/mm10/wgEncodeGencodeVM9.html mouse/mm10/wgEncodeGencodeVM10.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM10.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. [ONLY if it's going to be pushed] - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM10 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - -######################################################################### # LASTZ mouse/mm10 Chimp/panTro5 - (DONE - 2016-08-03 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzPanTro5.2016-08-03 cd /hive/data/genomes/mm10/bed/lastzPanTro5.2016-08-03 printf '# mouse vs chimp BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz BLASTZ_M=254 # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=10 # the default matrix is: @@ -12437,108 +12077,30 @@ -syntenicNet) > swap.log 2>&1 # real 98m32.623s cat fb.panTro5.chainMm10Link.txt # 965636631 bases of 3132620660 (30.825%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` panTro5 mm10) \ > rbest.log 2>&1 # real 560m21.432s ######################################################################### # Crispr track. See ../crisprTrack/README.txt (2016-09-15 max) # Command: doCrispr.sh mm10 ensGene ############################################################################## -######################################################################### -2016-10-27: import of UCSC GENCODE group processing of GENCODE VM11 (markd) - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM11 - cd /hive/data/genomes/mm10/bed/gencodeVM11 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructions in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM11.ra - cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM11.html - - # edit these plus mouse/mm10/trackDb.wgEncode.ra - # - set priorities in wgEncodeGencodeVM11.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM11 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - -############################################################################## -2016-12-08: import of UCSC GENCODE group processing of GENCODE VM12 (markd) - No being pushed to RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM12 - cd /hive/data/genomes/mm10/bed/gencodeVM12 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv- check to see if sizes make sense - - ## Copy and update trackDb files from previous release. - ## Change version and use lower priority so it sorts to top of - ## super track page. Follow instructions in ra file to ensure - ## filters are correct. - cd kent/src/hg/makeDb/trackDb - cp mouse/mm10/wgEncodeGencodeVM11.ra mouse/mm10/wgEncodeGencodeVM12.ra - cp mouse/mm10/wgEncodeGencodeVM11.html mouse/mm10/wgEncodeGencodeVM12.html - - # edit these plus mouse/mm10/trackDb.ra - # - set priorities in wgEncodeGencodeVM12.ra tracks so newest shows up first - # priority - set to previous version priority minus 0.001 - # searchPriority - set each to previous minus 0.001 - # - make current track default to pack and hide previous [ONLY if it's going to be pushed] - # superTrack wgEncodeGencodeSuper pack - # - Update wgEncodeGencodeSuper.html to describe new release and to - # pick up other updates. - - # DID NOT UPDATE all.joiner SINCE NOT BEING PUSHED PUBLIC - # update all.joiner and validate - # look for the last section `begin Gencode V??' in all.joiner - # and copy and update version - # repeat this until happy, editing minCheck as needed - # output in check/joiner.out - cd /hive/data/genomes/mm10/bed/gencodeVM12 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - ############################################################################################ # Mouse strains VCF (DONE - 2016-11-08 - Hiram) mkdir /hive/data/genomes/mm10/bed/strainsVCF cd /hive/data/genomes/mm10/bed/strainsVCF # download files: wget --timestamping \ ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi wget --timestamping \ ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi wget --timestamping \ ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz @@ -13273,58 +12835,30 @@ mkdir /hive/data/genomes/chrPic2/bed/blastz.mm10.swap cd /hive/data/genomes/chrPic2/bed/blastz.mm10.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzChrPic2.2017-04-05/DEF \ -syntenicNet -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -swap -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 & # real 12m2.676s cat fb.chrPic2.chainMm10Link.txt # 106063993 bases of 2173204089 (4.881%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` chrPic2 mm10) \ > rbest.log 2>&1 & # real 110m9.546s -######################################################################### -2017-04-16: import of UCSC GENCODE group processing of GENCODE VM13 (markd) - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM13 - pushd /hive/data/genomes/mm10/bed/gencodeVM13 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M13 88 'March 2017' - - # edit mouse/mm10/trackDb.ra to add new .ra file include - make DBS=mm10 - - # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' - # to describe new release. [ONLY if it's going to be pushed] - - # edit all.joiner to add ~/tmp/gencodeVM13.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM13 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all ############################################################################## # LASTZ Chinese hamster ovary cell line CHO-K1 criGriChoV1 # (DONE - 2017-04-13 - Hiram) # establish a screen to control this job screen -S mm10criGriChoV1 mkdir /hive/data/genomes/mm10/bed/lastzCriGriChoV1.2017-04-13 cd /hive/data/genomes/mm10/bed/lastzCriGriChoV1.2017-04-13 printf '# Chinese hamster ovary cell line vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 @@ -15002,58 +14536,30 @@ /gbdb/mm10/ncbiRefSeq/seqNcbiRefSeq.rna.fa # now have clean pslCheck, verify both with the file and the seq table: faSize -detailed /gbdb/mm10/ncbiRefSeq/seqNcbiRefSeq.rna.fa \ | pslCheck -querySizes=stdin -targetSizes=../../../chrom.sizes \ -db=mm10 ncbiRefSeqPsl # checked: 85224 failed: 0 errors: 0 hgsql -N -e 'select acc,size from seqNcbiRefSeq;' mm10 \ | pslCheck -querySizes=stdin -targetSizes=../../../chrom.sizes \ -db=mm10 ncbiRefSeqPsl # checked: 85224 failed: 0 errors: 0 ############################################################################## -2017-05-31: import of UCSC GENCODE group processing of GENCODE VM14 (markd) - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM14 - pushd /hive/data/genomes/mm10/bed/gencodeVM14 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M14 89 'May 2017' - - # edit mouse/mm10/trackDb.wgEncode.ra to add new .ra file include - make DBS=mm10 - - # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' - # to describe new release. [ONLY if it's going to be pushed] - - # edit all.joiner to add ~/tmp/gencodeVM14.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM14 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all -############################################################################## # LASTZ zebrafish danRer11 (DONE - 2017-06-12 - Chris) # establish a screen to control this job screen -S mm10danRer11 mkdir /hive/data/genomes/mm10/bed/lastzDanRer11.2017-06-12 cd /hive/data/genomes/mm10/bed/lastzDanRer11.2017-06-12 printf '# mouse vs. zebrafish BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 @@ -15509,61 +15015,30 @@ #1968 funcElems.gff # Transform GFF to BED+ ~/kent/src/hg/utils/automation/parseRefSeqFuncElems funcElems.gff /dev/stdout \ | sort -k1,1 -k2n,2n > refSeqFuncElems.bed wc -l refSeqFuncElems.bed #1968 refSeqFuncElems.bed # Make bigBed and link from /gbdb bedToBigBed -tab -type=bed9+7 -as=$HOME/kent/src/hg/lib/refSeqFuncElems.as \ refSeqFuncElems.bed /hive/data/genomes/mm10/chrom.sizes refSeqFuncElems.bb rm -f /gbdb/mm10/ncbiRefSeq/refSeqFuncElems.bb ln -s `pwd`/refSeqFuncElems.bb /gbdb/mm10/ncbiRefSeq/ ############################################################################## -2017-09-15: import of UCSC GENCODE group processing of GENCODE VM15 (markd) - # not to push to the RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM15 - pushd /hive/data/genomes/mm10/bed/gencodeVM15 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M15 90 'Aug 2017' - - # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' - # to describe new release. [ONLY if it's going to be pushed] - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM15.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM15 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all - -############################################################################## # ncbiRefSeq composite (DONE - 2017-11-16 - Angie) # Previously done 2017-09-28; redone 11-16 to include mito "rna" from chrM genomic seq mkdir /hive/data/genomes/mm10/bed/ncbiRefSeq.p5.2017-11-16 cd /hive/data/genomes/mm10/bed/ncbiRefSeq.p5.2017-11-16 time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ refseq vertebrate_mammalian Mus_musculus \ GCF_000001635.25_GRCm38.p5 mm10) > do.log 2>&1 & tail -f do.log # *** All done ! Elapsed time: 17m36s # real real 17m35.651s cat fb.ncbiRefSeq.mm10.txt # 105516336 bases of 2652783500 (3.978%) in intersection @@ -16068,62 +15543,30 @@ time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm10/bed/lastzEulMac1.2017-10-05/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 64m52.738s cat fb.eulMac1.chainMm10Link.txt # 895308387 bases of 2101039320 (42.613%) in intersection time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` eulMac1 mm10) \ > rbest.log 2>&1 # real 267m17.552s ############################################################################## -2017-12-17: import of UCSC GENCODE group processing of GENCODE VM16 (markd) - # being push to the RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM16 - pushd /hive/data/genomes/mm10/bed/gencodeVM16 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017' - - # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' - # to describe new release. [ONLY if it's going to be pushed] - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM16.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM16 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - -############################################################################## # LASTZ Damara mole rat vs. mouse/Mm10 (DONE - 2018-01-01 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzFukDam1.2018-01-01 cd /hive/data/genomes/mm10/bed/lastzFukDam1.2018-01-01 printf '# Damara mole rat vs. mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Damara mole rat SEQ2_DIR=/hive/data/genomes/fukDam1/fukDam1.2bit SEQ2_LEN=/hive/data/genomes/fukDam1/chrom.sizes @@ -16559,52 +16002,30 @@ # real 7m2.754s cat fb.petMar3.chainMm10Link.txt # 39217857 bases of 1043181598 (3.759%) in intersection cat fb.petMar3.chainSynMm10Link.txt # 1381239 bases of 1043181598 (0.132%) in intersection time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` petMar3 mm10) \ > rbest.log 2>&1 & # real 206m59.727s cat fb.petMar3.chainRBestMm10Link.txt # 21335101 bases of 1043181598 (2.045%) in intersection ######################################################################### -2018-03-08: update UCSC GENCODE VM16 to include protein id (for VAI) and fix PAR tag - -cd /hive/data/genomes/mm10/bed/gencodeVM16 - -# save existing data -mkdir -p prev/pre-proteinId -mv tables/wgEncodeGencodeAttrsVM16.tab tables/wgEncodeGencodeTagVM16.tab prev/pre-proteinId/ -mv loaded/wgEncodeGencodeAttrsVM16.tab.loaded loaded/wgEncodeGencodeTagVM16.tab.loaded prev/pre-proteinId/ -mv data/gencode.tsv prev/pre-proteinId/ -cp -p data/gencode.vM16.transcriptionSupportLevel.tab prev/pre-proteinId/ - -# edit gencodeLoad.mk to set mm10 as target - -# get gencode.tsv without rebuild TSL file or loading tables that don't change -~markd/compbio/ccds/ccds2/output/bin/x86_64/opt/gencodeGxfToAttrs --keepGoing data/release_M16/gencode.vM16.chr_patch_hapl_scaff.annotation.gtf.gz data/gencode.tsv -make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk loaded/wgEncodeGencodeAttrsVM16.tab.loaded loaded/wgEncodeGencodeTagVM16.tab.loaded - -# 2018-03-19: update search to include protein id -cd kent/src/hg/makeDb/trackDb -../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017' - -######################################################################### # lastz garter snake/thaSir1 (DONE - 2018-03-13 - Hiram) # establish a screen to control this job with a name to indicate what it is screen -S mm10ThaSir1 mkdir /hive/data/genomes/mm10/bed/lastzThaSir1.2018-03-13 cd /hive/data/genomes/mm10/bed/lastzThaSir1.2018-03-13 # note: first time with this new 1.04.00 version of lastz printf '# Mouse vs. garter snake BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_M=50 BLASTZ_Q=/scratch/data/blastz/HoxD55.q @@ -17235,63 +16656,30 @@ -syntenicNet) > swap.log 2>&1 & # real 67m0.560s cat fb.balAcu1.chainMm10Link.txt # 832845143 bases of 2286657046 (36.422%) in intersection cat fb.balAcu1.chainSynMm10Link.txt # 802734600 bases of 2286657046 (35.105%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` balAcu1 mm10) > rbest.log 2>&1 & # real 241m51.110s cat fb.balAcu1.chainRBest.Mm10.txt # 810427625 bases of 2286657046 (35.442%) in intersection -######################################################################### -2018-07-01: import of UCSC GENCODE group processing of GENCODE VM17 (markd) - # not being push to the RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM17 - pushd /hive/data/genomes/mm10/bed/gencodeVM17 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M17 92 'Mar 2018' - - ## only if being pushed to RR: - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM17.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM17 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - ############################################################################## # LASTZ mouse/mm10 Axolotl/ambMex1 - (DONE - 2018-07-09 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzAmbMex1.2018-07-09 cd /hive/data/genomes/mm10/bed/lastzAmbMex1.2018-07-09 printf '# mouse vs Axolotl BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_M=254 # default BLASTZ_Q score matrix: # A C G T # A 91 -114 -31 -123 # C -114 100 -125 -31 # G -31 -125 100 -114 # T -123 -31 -114 91 @@ -17352,66 +16740,30 @@ cat fb.ambMex1.chainSynMm10Link.txt # 2893381 bases of 28366694468 (0.010%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` ambMex1 mm10) > rbest.log 2>&1 & # real 568m10.621s # something odd went haywire at the download step time (doRecipBest.pl -load -continue=download -workhorse=hgwdev -buildDir=`pwd` ambMex1 mm10) > download.log 2>&1 & # real 3m16.404s cat fb.ambMex1.chainRBest.Mm10.txt # 38584422 bases of 28366694468 (0.136%) in intersection ############################################################################## -2018-08-03: import of UCSC GENCODE group processing of GENCODE VM18 (markd) - # being push to the RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM18 - pushd /hive/data/genomes/mm10/bed/gencodeVM18 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M18 93 'July 2018' - - ## only if being pushed to RR: - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM18.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM18 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - - cd ~/kent/src/hg/makeDb/trackDb - make alpha DBS=mm10 - -############################################################################## # LASTZ mouse/mm10 vs. chicken/galGal6 - (DONE - 2018-10-12 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzGalGal6.2018-10-12 cd /hive/data/genomes/mm10/bed/lastzGalGal6.2018-10-12 printf "# Mouse vs. chicken BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_Q=/scratch/data/blastz/HoxD55.q # A C G T # 91 -90 -25 -100 # -90 100 -100 -25 # -25 -100 100 -90 # -100 -25 -90 91 @@ -17532,67 +16884,30 @@ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -syntenicNet) > swap.log 2>&1 & # real 41m22.962s cat fb.bosTau9.chainMm10Link.txt # 695248613 bases of 2715853792 (25.600%) in intersection cat fb.bosTau9.chainSynMm10Link.txt # 660591041 bases of 2715853792 (24.324%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` bosTau9 mm10) > rbest.log 2>&1 & # real 204m36.465s cat fb.bosTau9.chainRBest.Mm10.txt # 667305554 bases of 2715853792 (24.571%) in intersection -######################################################################### -2018-11-10: import of UCSC GENCODE group processing of GENCODE VM19 (markd) - # not being push to the RR - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM19 - pushd /hive/data/genomes/mm10/bed/gencodeVM19 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M19 94 'Oct 2018' - - ## only if being pushed to RR: - (skipped) - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: (SKIPPED) - # edit all.joiner to add ~/tmp/gencodeVM19.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM19 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - - cd ~/kent/src/hg/makeDb/trackDb - make alpha DBS=mm10 - ############################################################################## # LASTZ mouse/mm10 vs. Japanese quail/cotJap2 - (DONE - 2018-11-15 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzCotJap2.2018-11-15 cd /hive/data/genomes/mm10/bed/lastzCotJap2.2018-11-15 printf "# Mouse vs. Japanese quail BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz BLASTZ_Y=3400 BLASTZ_L=6000 BLASTZ_K=2200 BLASTZ_Q=/scratch/data/blastz/HoxD55.q # A C G T # 91 -90 -25 -100 # -90 100 -100 -25 # -25 -100 100 -90 @@ -17648,67 +16963,30 @@ cat fb.cotJap2.chainSynMm10Link.txt # 66583746 bases of 917263224 (7.259%) in intersection # mistakenly started this on ku, it failed at the download step since # it could not see the /gbdb/mm10/ hierarchy: time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` cotJap2 mm10) > rbest.log 2>&1 & # real 79m48.767s # continue on hgwdev time (doRecipBest.pl -load -workhorse=hgwdev -continue=download -buildDir=`pwd` cotJap2 mm10) > rbest.download.log 2>&1 & # real 1m40.970s cat fb.cotJap2.chainRBest.Mm10.txt # 76078816 bases of 917263224 (8.294%) in intersection -############################################################################## -2018-11-30: import of UCSC GENCODE group processing of GENCODE VM20 prerelease (markd) - # This is a prerelease for testing and is *not* to pushed until the final release. - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM20 - pushd /hive/data/genomes/mm10/bed/gencodeVM20 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M20 95 'Dec 2018' - - ## only if being pushed to RR: - (skipped) - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: (SKIPPED) - # edit all.joiner to add ~/tmp/gencodeVM20.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM20 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - - cd ~/kent/src/hg/makeDb/trackDb - make alpha DBS=mm10 - ######################################################################### 2019-01-17: tabula muris track (max) # download 7Tb of data from Amazon, using token, CZI pays (got token by email, via Angela Pisco, James Webber) export AWS_ACCESS_KEY_ID=xxxxx export AWS_SESSION_TOKEN=xxxxx aws s3 sync s3://czbiohub-tabula-muris/tabula_muris_bam_files/ . --delete cd ~/projects/czi/cbData/ucsc/tabulaMuris csvToTab TM_facs_metadata.csv > TM_facs_metadata.tsv cat TM_facs_metadata.csv | tr '.' '-' | csvToTab > TM_facs_metadata.fix.tsv # this is not necessary anymore, the new mm10.sizes file comes with cbTrackHub and # includes the ERCCs hgsql -N -e 'select alias,chrom from chromAlias;' mm10 > mm10.chromAlias.tab faSize ERCC92.fa -detailed > ERCC.sizes cat /hive/data/genomes/mm10/chrom.sizes ERCC.sizes > mm10ercc.sizes @@ -17875,105 +17153,30 @@ # about 6 minutes rm -rf exonAA exonNuc export mz=multiz60way export gp=knownCanonical export db=mm10 export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments mkdir -p $pd ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz cd $pd md5sum *.fa.gz > md5sum.txt ############################################################################## -2019-04-08: import of UCSC GENCODE group processing of GENCODE VM20 (markd) - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM21 - pushd /hive/data/genomes/mm10/bed/gencodeVM21 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M21 96 'Apr 2019' - - ## only if being pushed to RR: - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM21.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM21 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - - cd ~/kent/src/hg/makeDb/trackDb - make alpha DBS=mm10 - - # commit all - # if pushing public, add ticket and MARK QA READY - -######################################################################### -2019-07-03: import of UCSC GENCODE group processing of GENCODE VM22 (markd) - # Replaced import of pre-release - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM22 - pushd /hive/data/genomes/mm10/bed/gencodeVM22 - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - ## gencode-cmp.tsv check to see if sizes make sense - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M22 97 'June 2019' - - ## only if being pushed to RR: - # Update mouse/mm10/wgEncodeGencodeSuper.html - # Update 'Release Notes' to describe new release. - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM22.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM22 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 - - # commit all and make push request, the file tables.lst will have the - # list of tables for the push request. - - cd ~/kent/src/hg/makeDb/trackDb - make alpha DBS=mm10 - - # commit all - # if pushing public, add ticket and MARK QA READY - -############################################################################## # LASTZ Rat regenRn0 (DONE - 2019-07-01 - Jonathan) mkdir /hive/data/genomes/mm10/bed/lastzRegenRn0.2019-07-01 cd /hive/data/genomes/mm10/bed/lastzRegenRn0.2019-07-01 printf '# rat vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/scratch/data/mm10/mm10.2bit SEQ1_LEN=/scratch/data/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rat RegenRn0 SEQ2_DIR=/hive/data/genomes/regenRn0/regenRn0.2bit SEQ2_LEN=/hive/data/genomes/regenRn0/chrom.sizes @@ -18073,85 +17276,30 @@ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 52m48.045s cat fb.rheMac10.chainMm10Link.txt # 918551088 bases of 2936892733 (31.276%) in intersection cat fb.rheMac10.chainSynMm10Link.txt # 876230433 bases of 2936892733 (29.835%) in intersection time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 mm10) > rbest.log 2>&1 # real 303m40.303s cat fb.rheMac10.chainRBest.Mm10.txt # 878542993 bases of 2936892733 (29.914%) in intersection -############################################################################## -2019-08-30: import of UCSC GENCODE group processing of GENCODE VM23 (markd) - # PRE-RELEASE - - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM23 - pushd /hive/data/genomes/mm10/bed/gencodeVM23 - - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. Results are in gencode-cmp.tsv - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M23 98 'Sept 2019' - - # If being pushed public, update 'Release Notes' in - # human/mm10/wgEncodeGencodeSuper.html - - # edit human/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM23.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM23 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - - # commit all - # if pushing public: add ticket and MARK QA READY - -2019-08-30: repeat above for final release - mv /hive/data/genomes/mm10/bed/gencodeVM23 /hive/data/genomes/mm10/bed/gencodeVM23pre - # redo do above imports - - for t in tables/* ; do cmp ../gencodeVM23pre/$t $t ; done - - Changes: - wgEncodeGencode2wayConsPseudoVM23.gp - wgEncodeGencodeAttrsVM23.tab - wgEncodeGencodePolyaVM23.gp - wgEncodeGencodeTagVM23.tab - only attrs and maybe tags matter to hgGene gencode - - mkdir pre-diffs - diff ../gencodeVM23pre/tables/wgEncodeGencodeAttrsVM23.tab tables/wgEncodeGencodeAttrsVM23.tab >pre-diffs/wgEncodeGencodeAttrsVM23.diff - diff ../gencodeVM23pre/tables/wgEncodeGencodeTagVM23.tab tables/wgEncodeGencodeTagVM23.tab >pre-diffs/wgEncodeGencodeTagVM23.diff - - # wgEncodeGencodeAttrsVM23: experimental confirmation level changed on a few pseudogenes - # wgEncodeGencodeTagVM23: pseudo_consens changed on a few pseudogenes. - - ######################################################################### # LASTZ Rat regenRn1 (DONE - 2019-09-12 - Hiram) mkdir /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-12 cd /hive/data/genomes/mm10/bed/lastzRegenRn1.2019-09-12 printf '# rat vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rat RegenRn1 SEQ2_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit @@ -18264,62 +17412,30 @@ Longest finished job: 1966s 32.77m 0.55h 0.02d Submission to last job: 15067s 251.12m 4.19h 0.17d # offTargets: Completed: 147394 of 147394 jobs CPU time in finished jobs: 2213680s 36894.66m 614.91h 25.62d 0.070 y IO & Wait Time: 2663355s 44389.25m 739.82h 30.83d 0.084 y Average job time: 33s 0.55m 0.01h 0.00d Longest finished job: 68s 1.13m 0.02h 0.00d ######################################################################### # For ENCODE 3 tracks, see doc/encode3/mouse.txt ############################################################################## -2019-11-16: import of UCSC GENCODE group processing of GENCODE VM24 PRE-RELEASE (markd) - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24 - pushd /hive/data/genomes/mm10/bed/gencodeVM24 - - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. Results are in gencode-cmp.tsv - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M24 99 'Nov 2019' - - # If being pushed public, update 'Release Notes' in - # human/mm10/wgEncodeGencodeSuper.html - - # edit human/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM24.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM24 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - - # commit all - # if pushing public: add ticket and MARK QA READY - -############################################################################## # LASTZ Gorilla gorGor6 (DONE - 2019-11-20 - Hiram) # establish a screen to control this job screen -S mm10gorGor6 mkdir /hive/data/genomes/mm10/bed/lastzGorGor6.2019-11-20 cd /hive/data/genomes/mm10/bed/lastzGorGor6.2019-11-20 printf '# mouse vs. gorilla BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=1 @@ -18429,111 +17545,41 @@ # real 101m20.296s cat fb.regenCho1.chainMm10Link.txt # 1522181082 bases of 2266312740 (67.166%) in intersection cat fb.regenCho1.chainSynMm10Link.txt # 1397889394 bases of 2266312740 (61.681%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev regenCho1 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 660m29.571s cat fb.regenCho1.chainRBest.Mm10.txt # 1396267649 bases of 2266312740 (61.610%) in intersection ############################################################################## -2020-01-16: import of UCSC GENCODE group processing of GENCODE VM24 (markd) - # deprecate pre-release - mv /hive/data/genomes/mm10/bed/gencodeVM24 /hive/data/genomes/hg38/bed/gencodeVM24pre - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24 - pushd /hive/data/genomes/mm10/bed/gencodeVM24 - - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. Results are in gencode-cmp.tsv - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M24 99 'Jan 2020' - - # If being pushed public, update 'Release Notes' in - # mouse/mm10/wgEncodeGencodeSuper.html - - # edit human/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM24.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM24 - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - - # check tracks in browser sandbox - # commit all - make DBS=mm10 alpha - # if pushing public: add ticket and MARK QA READY - -############################################################################## clinvar lift, done, Fri Jan 31 06:12:46 PST 2020, max doClinvarLift mm10 featureBits hg38 clinvarLift.bed 620623 bases of 3095998939 (0.020%) in intersection wc -l clinvarLift.bed 610774 clinvarLift.bed featureBits mm10 clinvarLift.mm10.bed 581378 bases of 2652783500 (0.022%) in intersection wc -l clinvarLift.mm10.bed 575023 clinvarLift.mm10.bed ############################################################################## -2020-03-11: import of UCSC GENCODE group processing of GENCODE VM25 pre-release (markd) - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions - - # download, build and load tables - mkdir -p /hive/data/genomes/mm10/bed/gencodeVM25Pre - pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre - - (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& - - # compare tables from previous release to see if number changed makes - # sense. Results are in gencode-cmp.tsv - - # generate trackDb and joiner blurb - pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M25 100 'March 2020' - - # If being pushed public, update 'Release Notes' if pushing puyblic. - # mouse/mm10/wgEncodeGencodeSuper.html - - # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include - make DBS=mm10 - - ## only if being pushed to RR: - # edit all.joiner to add ~/tmp/gencodeVM25.joiner - # verify with: - pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre - make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck - - # check tracks in browser sandbox - # commit all - make DBS=mm10 alpha - # if pushing public: add ticket and MARK QA READY - -############################################################################## # LASTZ Southern sea otter enhLutNer1 (DONE - 2020-04-16 - Jonathan) # establish a screen to control this job mkdir /hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15 cd /hive/data/genomes/mm10/bed/lastzEnhLutNer1.2020-04-15 printf '# Southern sea otter vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz # TARGET: Mouse Mm10 SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40