fe2d1d757565d0141b91e6c6856a8fcf06579a3f hiram Mon Aug 19 13:20:13 2019 -0700 note copy and paste error in file name construction for phyloP60way download files #21388 diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt index ef96d4e..245ecc9 100644 --- src/hg/makeDb/doc/mm10.txt +++ src/hg/makeDb/doc/mm10.txt @@ -7256,30 +7256,31 @@ # Completed: 2709 of 2709 jobs # CPU time in finished jobs: 206723s 3445.39m 57.42h 2.39d 0.007 y # IO & Wait Time: 256366s 4272.76m 71.21h 2.97d 0.008 y # Average job time: 171s 2.85m 0.05h 0.00d # Longest finished job: 487s 8.12m 0.14h 0.01d # Submission to last job: 1926s 32.10m 0.54h 0.02d cd /hive/data/genomes/mm10/bed/multiz60way/consPhyloP/glire mkdir downloads for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` do echo "working: $D" find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ | gzip -c > downloads/${D}.phastCons60way.glire.wigFix.gz +XXX - copy and paste error, should have been phyloP60way and not phastCons done time (zcat downloads/chr*.wigFix.gz \ | wigEncode stdin phyloP60wayGlire.wig phyloP60wayGlire.wib \ > wigEncode.log 2>&1) & # Converted stdin, upper limit 1.17, lower limit -4.35 # real 20m31.753s export sizeG=188743680 ulimit -d $sizeG ulimit -v $sizeG time (zcat downloads/chr*.wigFix.gz \ | wigToBigWig stdin ../../../../chrom.sizes phyloP60wayGlire.bw) & # real 37m9.063s bigWigInfo phyloP60wayGlire.bw @@ -7359,30 +7360,31 @@ # Completed: 2709 of 2709 jobs # CPU time in finished jobs: 542547s 9042.45m 150.71h 6.28d 0.017 y # IO & Wait Time: 75914s 1265.23m 21.09h 0.88d 0.002 y # Average job time: 228s 3.80m 0.06h 0.00d # Longest finished job: 430s 7.17m 0.12h 0.00d # Submission to last job: 4149s 69.15m 1.15h 0.05d cd /hive/data/genomes/mm10/bed/multiz60way/consPhyloP/euarchontoglires mkdir downloads for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` do echo "working: $D" find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ | gzip -c > downloads/${D}.phastCons60way.euarchontoglires.wigFix.gz +XXX - copy and paste error, should have been phyloP60way and not phastCons done time (zcat downloads/chr*.wigFix.gz \ | wigEncode stdin phyloP60wayEuarchontoGlires.wig phyloP60wayEuarchontoGlires.wib \ > wigEncode.log 2>&1) & # Converted stdin, upper limit 1.75, lower limit -12.70 # real 10m52.064s export sizeG=188743680 ulimit -d $sizeG ulimit -v $sizeG time (zcat downloads/chr*.wigFix.gz \ | wigToBigWig stdin ../../../../chrom.sizes phyloP60wayEuarchontoGlires.bw) & # real 26m47.912s bigWigInfo phyloP60wayEuarchontoGlires.bw @@ -7466,30 +7468,31 @@ # Completed: 2709 of 2709 jobs # CPU time in finished jobs: 307901s 5131.68m 85.53h 3.56d 0.010 y # IO & Wait Time: 42937s 715.62m 11.93h 0.50d 0.001 y # Average job time: 130s 2.16m 0.04h 0.00d # Longest finished job: 234s 3.90m 0.07h 0.00d # Submission to last job: 5975s 99.58m 1.66h 0.07d cd /cluster/data/mm10/bed/multiz60way/consPhyloP/run.phyloP/primate mkdir downloads for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` do echo "working: $D" find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ | gzip -c > downloads/${D}.phastCons60way.primate.wigFix.gz +XXX - copy and paste error, should have been phyloP60way and not phastCons done time (zcat downloads/chr*.wigFix.gz \ | wigEncode stdin phyloP60wayPrimate.wig phyloP60wayPrimate.wib \ > wigEncode.log 2>&1) & # real 9m37.055s # Converted stdin, upper limit 0.93, lower limit -10.63 export sizeG=188743680 ulimit -d $sizeG ulimit -v $sizeG time (zcat downloads/chr*.wigFix.gz \ | wigToBigWig stdin ../../../../chrom.sizes phyloP60wayPrimate.bw) & # real 24m18.842s bigWigInfo phyloP60wayPrimate.bw version: 4 @@ -7571,30 +7574,31 @@ # Completed: 2709 of 2709 jobs # CPU time in finished jobs: 1188036s 19800.60m 330.01h 13.75d 0.038 y # IO & Wait Time: 209859s 3497.65m 58.29h 2.43d 0.007 y # Average job time: 516s 8.60m 0.14h 0.01d # Longest finished job: 1672s 27.87m 0.46h 0.02d # Submission to last job: 6336s 105.60m 1.76h 0.07d cd /hive/data/genomes/mm10/bed/multiz60way/consPhyloP/placental mkdir downloads for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` do echo "working: $D" find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ | gzip -c > downloads/${D}.phastCons60way.placental.wigFix.gz +XXX - copy and paste error, should have been phyloP60way and not phastCons done time (zcat downloads/chr*.wigFix.gz \ | wigEncode stdin phyloP60wayPlacental.wig phyloP60wayPlacental.wib \ > wigEncode.log 2>&1) & # Converted stdin, upper limit 3.30, lower limit -20.00 # real 11m54.289s export sizeG=188743680 ulimit -d $sizeG ulimit -v $sizeG time (zcat downloads/chr*.wigFix.gz \ | wigToBigWig stdin ../../../../chrom.sizes phyloP60wayPlacental.bw \ > bigWig.log 2>&1) & # real 28m4.576s bigWigInfo phyloP60wayPlacental.bw version: 4 @@ -7676,30 +7680,31 @@ # Completed: 2709 of 2709 jobs # CPU time in finished jobs: 1825414s 30423.56m 507.06h 21.13d 0.058 y # IO & Wait Time: 211040s 3517.34m 58.62h 2.44d 0.007 y # Average job time: 752s 12.53m 0.21h 0.01d # Longest finished job: 1530s 25.50m 0.42h 0.02d # Submission to last job: 6045s 100.75m 1.68h 0.07d cd /hive/data/genomes/mm10/bed/multiz60way/consPhyloP/vertebrate mkdir downloads for D in `ls -d wigFix/chr* | sed -e 's#wigFix/##'` do echo "working: $D" find ./wigFix/${D} -type f | sed -e "s#^./##; s#\.# d #g; s#-# m #;" \ | sort -k1,1 -k3,3n | sed -e "s# d #.#g; s# m #-#g;" | xargs cat \ | gzip -c > downloads/${D}.phastCons60way.vertebrate.wigFix.gz +XXX - copy and paste error, should have been phyloP60way and not phastCons done time (zcat downloads/chr*.wigFix.gz \ | wigEncode stdin phyloP60wayVertebrate.wig phyloP60wayVertebrate.wib \ > wigEncode.log 2>&1) & # Converted stdin, upper limit 7.53, lower limit -20.00 # real 12m2.774s export sizeG=188743680 ulimit -d $sizeG ulimit -v $sizeG time (zcat downloads/chr*.wigFix.gz \ | wigToBigWig stdin ../../../../chrom.sizes phyloP60wayVertebrate.bw \ > bigWig.log 2>&1) & # real 27m6.791s