Tuesday 03/04/14

8:30a – 9:45a, 2:00p – 11:45p

computer stuff

• Copying files extremely slow. 335 Gb copy from ProBox 1 less than half done
• computer seems to have taken the night off. Splitdax was on like 115 of 136 at midnight and is now only on 128 of 136.
• canceled
  • 2013-12-28_PhWtPh, 2013-12-29_PhMPh, 2013-12-31_PhWtPh from ProBox6 to ProRAID
  • 2014-01-30_PhMPh and 2014-01-30_PhWtPh from AlistairRAID2 to ProRAID
• still copying 2014-01-09_PhM from ProBox1 to ProRAID. extremely slow. This folder needs some splitdax action too.

(cross-country skiing, 9:45a – 2:00p)

RC computing

• Bug fix: remote queue commands need to begin with #!/bin/bash not #!/bin/bash/.
• Fixed cufflinks file

  #!/bin/bash

  #SBATCH -n 1

  #SBATCH -t 1440

  #SBATCH -p general

  #SBATCH –mem=6000

  #SBATCH -o /n/home05/boettiger/out

  #SBATCH -e /n/home05/boettiger/err

  module load centos6/cufflinks-2.1.1.Linux_x86_64
  cufflinks –max-bundle-frags 90900900 -G /n/holyscratch/zhuang_lab/boettiger/gencode.v18.annotation.gtf /n/holyscratch/zhuang_lab/boettiger/IMR90.sam > /n/holyscratch/zhuang_lab/boettiger/outputCufflinks.txt 2> /n/holyscratch/zhuang_lab/boettiger/errorsCufflinks.txt

ChromatinCropper

• Found Bug!! props2D.mainArea*pixelSize should have been props2D.mainArea*pixelSize^2! For the most part this should just be a linear rescaling of the data.
• fixed bug, reran data. As expected, more-or-less a linear rescaling. Some adjustments due to sparicity of localizations results in minor relative shifts.