Biowulf High Performance Computing at the NIH
truffle on Biowulf

Fast and accurate shared segment detection and relatedness estimation in un- phased genetic data using TRUFFLE

Documentation
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 and run the program. Sample session:

[user@biowulf]$ sinteractive
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 ~]$ module load truffle

[user@cn3144 ~]$ truffle --vcf /usr/local/apps/truffle/TEST_DATA/fs-and-po-pairs-from-1000genomes.vcf.gz --segments --cpu $SLURM_CPUS_ON_NODE
     _               __  __ _       
    | |             / _|/ _| |      
    | |_ _ __ _   _| |_| |_| | ___  
    | __| '__| | | |  _|  _| |/ _ \ 
    | |_| |  | |_| | | | | | |  __/ 
     \__|_|   \__,_|_| |_| |_|\___| 
        
         - TRUFFLE v1.38 -    



***
*** Non-commerical and educational use license.
***


[*]  Options in effect: 
      -   Input file: /usr/local/apps/truffle/TEST_DATA/fs-and-po-pairs-from-1000genomes.vcf.gz
      -   Number of CPUs: 2

      -   Reporting threshold: all pairs

      -   Segment reporting: YES

      -   Input file name: /usr/local/apps/truffle/TEST_DATA/fs-and-po-pairs-from-1000genomes.vcf.gz
      -   Opening output file truffle.ibd  
      -   Opening output file truffle.segments  
      -   Number of samples: 47

      -   Allocation genotype vector  npeople=63 nvars=200000
      -   GenotypeMatrix: allocating 12 MB of memory
      -   Excluding variants with missing rate > 0.020 (1 samples)

      -   Excluding variants with allele frequency  < 0.060

      -   Reading chromosome 1 (pos=0)
      -   Reading chromosome 2 (pos=12291)
      -   Reading chromosome 3 (pos=24479)
      -   Reading chromosome 4 (pos=34767)
      -   Reading chromosome 5 (pos=44872)
      -   Reading chromosome 6 (pos=53948)
[...]
[*]  Genotype pre-processing duration:  506.32 ms 

 -  Compute IBD by IBS: (cpu=1/2) Nind = 47 Nvar = 155313
 -  Compute IBD by IBS: (cpu=2/2) Nind = 47 Nvar = 155313

[*] Finished processing 

      -   Total time for analysis was 0.02 minutes (1.1 seconds)

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. truffle.sh). For example:

#!/bin/bash
set -e
module load truffle
truffle --vcf /usr/local/apps/truffle/TEST_DATA/fs-and-po-pairs-from-1000genomes.vcf.gz --segments --cpu $SLURM_CPUS_ON_NODE

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=4g truffle.sh
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. truffle.swarm). For example:

truffle --vcf s1.vcf.gz --segments --cpu $SLURM_CPUS_ON_NODE --out s1
truffle --vcf s2.vcf.gz --segments --cpu $SLURM_CPUS_ON_NODE --out s2
truffle --vcf s3.vcf.gz --segments --cpu $SLURM_CPUS_ON_NODE --out s3

Submit this job using the swarm command.

swarm -f truffle.swarm -g 4 -t 4 --module truffle
where
-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 truffle Loads the truffle module for each subjob in the swarm