bcl2fastq demxuing on zcluster

bcl2fastq-on-zcluster.md

• create shell script to run configuration of job. Save the following as configure.sh:

  #!/bin/bash
  export LD_LIBRARY_PATH=/usr/local/boost/1.44.0/gcc447/lib:${LD_LIBRARY_PATH}
  
  cd /escratch4/tcg_tech2/tcg_tech2_Mar_03/test-ACN5P
  
  # create a basecalls directory to hold our output
  /usr/local/bcl2fastq/1.8.4/bin/configureBclToFastq.pl \
      --input-dir 150213_M02849_0082_000000000-ACN5P/Data/Intensities/BaseCalls/ \
      --out basecalls \
      --use-bases-mask Y*,I8,I8,Y* \
      --sample-sheet 150213_M02849_0082_000000000-ACN5P/Data/Intensities/BaseCalls/SampleSheet.csv
  

• submit the job to the queuing software:

    qsub -q rcc-30d configure.sh
  

• that should run and create the "basecalls" directory. look at the contents of the stderr file to make sure it's all green. If it's not, nuke the basecalls directory, fix the errors, and rerun the above:

  cat configure.sh.e7046793
  

• looks good. now lets create the actual demuxing script in file named make.sh bcl2fastq doesn't run that much better with 8 threads than 4, so just use 4. You could change to 8 here (be sure to change in both places). Save the following in make.sh. You only need to invoke make once (for all files):

  #!/bin/bash
  export OMP_NUM_THREADS=4
  export LD_LIBRARY_PATH=/usr/local/boost/1.44.0/gcc447/lib:${LD_LIBRARY_PATH}
  
  cd /escratch4/tcg_tech2/tcg_tech2_Mar_03/test-ACN5P/basecalls
  make -j 4
  

• submit the job to the queuing software:

    qsub -q rcc-30d -pe thread 4 make.sh
  

• data are going to be in basecalls/Project_default/, where the "default" part of that name is the project name you used.