Biowulf High Performance Computing at the NIH
eager on Biowulf

Eager is a tool for the efficient reconstruction of ancient genomes. It includes a GUI to create XML configuration files and a command line interface to run the analysis pipeline.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session with a graphical connection - either from an NX session or with X11 forwarding.

[user@biowulf]$ sinteractive --cpus-per-task=6 --mem=30g --gres=lscratch:50
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID

We will use a medieval Mycobacterium leprae sample from Schuenemann et al.

[user@cn3144]$ cp -Lr ${EAGER_TEST_DATA:-none} data
[user@cn3144]$ # start the GUI
[user@cn3144]$ singularity exec -B $PWD/data:/data $EAGER_IMG eager

Follow the tutorial in the eager docs to create a configuration file. Note that the data directory is mounted at /data inside the container. Then run the pipeline with the command line interface

[user@cn3144]$ singularity exec -B $PWD/data:/data $EAGER_IMG eagercli /data/Results
Found 1 input configuration files.
Processing file # 1
Schaffa, Schaffa, Genome baua!
Checking for file at path: /data/References/NC_011896.dict

# ModulePoolPaths: [/data/RAW/sk8/sk8_R1.fastq.gz, /data/RAW/sk8/sk8_R2.fastq.gz]
# Module that will be now executed: CreateResultsDirectories
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226

Batch job
Most jobs should be run as batch jobs.

Create a configuration file for a run either using the GUI or some other way. Then create a batch script file. For example:

module load eager/1.92

singularity exec -B ${datad}:/data $EAGER_IMG eagercli /data/Results/sample1/2018-09-05-16-27-EAGER.xml

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=32g
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. eager.swarm). For example:

singularity exec -B /data/$USER/eager:/data $EAGER_IMG eagercli /data/Results/sample1/2018-09-05-16-27-EAGER.xml
singularity exec -B /data/$USER/eager:/data $EAGER_IMG eagercli /data/Results/sample2/2018-09-05-16-27-EAGER.xml
singularity exec -B /data/$USER/eager:/data $EAGER_IMG eagercli /data/Results/sample3/2018-09-05-16-27-EAGER.xml

Submit this job using the swarm command.

swarm -f eager.swarm -g 32 -t 4 --module eager/1.92
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module eager Loads the eager module for each subjob in the swarm