Genscan

Hard mask

Genscan works with hard masked sequence. All masked sequence is converted to N's. UCSC runs this as a cluster job, although it is a simple loop if you are willing to wait. The gensub2 template is:

#LOOP
./runOne.csh $(root1) ../hardMaskedFa/$(lastDir1)/$(file1)
#ENDLOOP

The runOne.csh script:

#!/bin/csh -ef
set chrom = $1
set result = $2
twoBitToFa /data/genomes/ricCom1/ricCom1.2bit:$chrom stdout \
 | maskOutFa stdin hard $result

C-shell script syntax here to manually construct a directory hierarchy to contain all the resulting hard masked fasta files and the chr.list file to use with gensub2:

mkdir -p /data/genomes/ricCom1/bed/genscan/run.hardMask
cd /data/genomes/ricCom1/bed/genscan/run.hardMask
mkdir -p ../hardMaskedFa
set perDirLimit = 4000
set ctgCount = `twoBitInfo /data/genomes/ricCom1/ricCom1.2bit stdout | wc -l`
set subDirCount = `echo $ctgCount | awk '{printf "%d", 1+$1/4000}'`
@ dirCount = 0
set dirName = `echo $dirCount | awk '{printf "%03d", $1}'`
@ perDirCount = 0
mkdir ../hardMaskedFa/$dirName
/bin/rm -f chr.list
/bin/touch chr.list
foreach chrom ( `twoBitInfo /data/genomes/ricCom1/ricCom1.2bit stdout | cut -f1` )
  if ($perDirCount < $perDirLimit) then
    @ perDirCount += 1
  else
    @ dirCount += 1
    set dirName = `echo $dirCount | awk '{printf "%03d", $1}'`
    set perDirCount = 1
    mkdir ../hardMaskedFa/$dirName
  endif
  echo $dirName/$chrom.fa >> chr.list
end

The gensub2 constructs the jobList:

gensub2 chr.list single template jobList

Typical parasol cluster run:

para make jobList
para check
para time > run.time
cat run.time
Completed: 25763 of 25763 jobs
CPU time in finished jobs:         90s       1.50m     0.02h    0.00d  0.000 y
IO & Wait Time:                 65875s    1097.92m    18.30h    0.76d  0.002 y
Average job time:                   3s       0.04m     0.00h    0.00d
Longest finished job:               6s       0.10m     0.00h    0.00d
Submission to last job:           259s       4.32m     0.07h    0.00d