HLab:Steps
Contents
Bcl – qseq - fastq
1. Get run folder name
from Cheryl. (RUN_NAME)
2. Create RUN_NAME directory
under /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/job_output (example: mkdir 120111_SN407_0185_BD0F1EABXX )
3. Make a config file (CONFIG_FILE)
In /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/ Copy the previous run’s config file and change the info in it to reflect the updated information. Basically, wherever you spot the run name of some old run in this file, change it to the current RUN_NAME. Give your own email address.
4. Submit jobs
In the same directory, i.e. /afs/bx.psu.edu/depot/data/hardison_lab/illumina/bcl_to_fastq/ run the following command:
submit-jobs CONFIG_FILE
This submits jobs to the cluster (persephone). Use qstat to check on progress. It will email at the start and end of each job. The error and output files are written to the directory you created under job_output. If a job errors out use qdel JOBID to delete it. (or qdel –u username to delete all jobs) The output qseq and fastq files will be in the location specified in the CONFIG_FILE. During the conversion to fastq the reads are filtered based on the pass filter field of the qseq file.
Run 32 finished in about 2 hours using less than 4G of RAM.
