SLab:Run Processing

454

rigs

• schuster-flx1
• schuster-flx2
• schuster-flx3
• schuster-flx4

on-rig processing

• run directories are stored in /data
  • /data/YYYY_MM_DD/R_YYYY_MM_DD_HH_MM_SS_RIGNAME_OPERATOR_RUNNAME
• when a run finishes processing, it calls the /usr/local/rig/bin/postAnalysisScript.sh script
  • rsync's run directory to s2:/zfs/md1k-4/data/sequencing/temp/454
  • ssh's to c1.persephone to submit job
    • depending on run
      • calls c1.persephone:/usr/local/bin/submit-signalProcessing.sh
      • calls c1.persephone:/usr/local/bin/submit-fullProcessing.sh
  • status email is sent to 454pipeline@bx.psu.edu
  • our postAnalysisScript.sh is kept in /home/adminrig/postAnalysisScript directory on each rig
    • revision controlled using rcs
      •  % co -l postAnalysisScript.sh
      •  % vi postAnalysisScript.sh
      •  % ci -u postAnalysisScript.sh
    • Makefile in this directory installs our version into /usr/local/rig/bin
      •  % make install

signal processing

• signal processing for runs is performed on the persephone cluster
• depending on run
  • uses qsub to submit job using c1.persephone:/usr/local/bin/signalProcessing.qsub
  • uses qsub to submit job using c1.persephone:/usr/local/bin/fullProcessing.qsub
• status email is sent to 454pipeline@bx.psu.edu

Before exiting signal processing jobs signal that processing is done by touching a file with the same name as the run directory:

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/temp/454/.processing_finished/RUN_DIR_NAME

staging

A cron job on s2 checks the /zfs/md1k-4/data/sequencing/temp/454/.processing_finished directory once a minute to see if any signal processing jobs have finished. When it finds a finished signal processing job, it moves it to the staging directory:

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/staging/454/RUN_DIR

Once the run has been copied to the staging directory, the files in the run directory are modified as needed to make sure they have the correct owner, group, and permissions.

archive

To archive a run, it needs to be moved into one of the archive folders (md1k-1, md1k-2, md1k-3 on s3) or (md1k-4, md1k-5, md1k-6 on s2).

The /zfs/md1k-N/archive filesystem is compressed and exported read-only.

s3:/zfs/md1k-{1,2,3}/archive/sequencing/454/YYYY/YYYY_MM_DD/
s2:/zfs/md1k-{4,5,6}/archive/sequencing/454/YYYY/YYYY_MM_DD/

After the run has been archived, the links in the following directory need to be modified to reflect the location of the run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/454

Illumina

systems

• illumina-ga

on-system processing

Samba is running on s2.persephone so that the Illumina GA can copy it's data directly to s2.

• The Illumina GA copies it's data to one of three locations (decided by the operator)
  • s2.persephone\\illumina-4 which is on s2.persephone:/zfs/md1k-4/data/illumina
  • s2.persephone\\illumina-5 which is on s2.persephone:/zfs/md1k-5/data/illumina
  • s2.persephone\\illumina-6 which is on s2.persephone:/zfs/md1k-5/data/illumina
• Using the current software, both image analysis and base calling are performed on-system
  • SCS2.5/RTA1.5
  • SCS2.6/RTA1.6

staging

After we receive an email from the operator informing us that a tun has completed, we copy it to the staging directory using one of these commands:

For runs that used illumina-4

% mv /zfs/md1k-4/data/illumina/RUN_NAME /zfs/md1k-4/data/sequencing/staging/illumina/RUN_NAME

For runs that used illumina-5

% mv /zfs/md1k-5/data/illumina/RUN_NAME /zfs/md1k-5/data/sequencing/staging/illumina/RUN_NAME

For runs that used illumina-4

% mv /zfs/md1k-6/data/illumina/RUN_NAME /zfs/md1k-6/data/sequencing/staging/illumina/RUN_NAME

We then create a symlink to the run in AFS: (replace md1k-4-data with md1k-5-data or md1k-6-data as necessary)

% cd /afs/.bx.psu.edu/depot/data/schuster_lab/sequencing/staging/illumina
% ln -s /nfs/s2.persephone.bx.psu.edu/md1k-4-data/sequencing/staging/illumina/RUN_NAME
% cd /afs/.bx.psu.edu/depot/data/schuster_lab/sequencing/archive/illumina/flat
% ln -s /nfs/s2.persephone.bx.psu.edu/md1k-4-data/sequencing/staging/illumina/RUN_NAME
% afs-control release data.schuster_lab

signal processing

beep

archive

To archive a run, it needs to be moved into one of the archive folders (md1k-1, md1k-2, md1k-3 on s3) or (md1k-4, md1k-5, md1k-6 on s2).

The /zfs/md1k-N/archive filesystem is compressed and exported read-only.

s3:/zfs/md1k-{1,2,3}/archive/sequencing/illumina/YYYY/YYYY_MM_DD/
s2:/zfs/md1k-{4,5,6}/archive/sequencing/illumina/YYYY/YYYY_MM_DD/

After the run has been archived, the links in the following directory need to be modified to reflect the location of the run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/illumina