Biowulf High Performance Computing at the NIH

a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis

Web site

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

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --gres=lscratch:10 
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 ~]$ mkdir /data/$USER/seqlinkage-example

[user@cn3144 ~]$ cd /data/$USER/seqlinkage-example

[user@cn3144 ~]$ module load seqlinkage
[+] Loading seqlinkage 1.0 on
[+] Loading singularity 2.2 on

[user@cn3144 ~]$ cp $SEQLINKAGE_HOME/example-data/seqlinkage-example* .

[user@cn3144 ~]$ seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN -j 4 --tempdir /lscratch/$SLURM_JOB_ID
MESSAGE: Binary trait detected in [/spin1/users/user/seqlinkage-example/seqlinkage-example.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 12 samples found in [/spin1/users/user/seqlinkage-example/seqlinkage-example.vcf.gz]
MESSAGE: 2 families with a total of 12 samples will be scanned for 25,305 pre-defined units
MESSAGE: 2 units (from 18 variants) processed; 3 Mendelian inconsistencies and 2 recombination events handled
MESSAGE: 25,302 units ignored due to absence in VCF file
MESSAGE: 1 units ignored due to absence of variation in samples
MESSAGE: Archiving regional marker data to directory [/spin1/users/user/seqlinkage-example/cache]
MESSAGE: 2 units will be converted to MERLIN format
MESSAGE: 2 units successfully converted to MERLIN format
MESSAGE: Archiving MERLIN format to directory [/spin1/users/user/seqlinkage-example/cache]
MESSAGE: Saving data to [/spin1/users/user/seqlinkage-example/LINKAGE]

[user@cn3144 ~]$ ls -l LINKAGE/MERLIN/
total 16
-rw-r--r-- 1 user staff  17 Jan 13 14:54 LINKAGE.chr1.dat
-rw-r--r-- 1 user staff 109 Jan 13 14:54
-rw-r--r-- 1 user staff 256 Jan 13 14:54 LINKAGE.chr1.ped
-rw-r--r-- 1 user staff  28 Jan 13 14:54 LINKAGE.chr16.dat
-rw-r--r-- 1 user staff 164 Jan 13 14:54
-rw-r--r-- 1 user staff 304 Jan 13 14:54 LINKAGE.chr16.ped

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

Running a single SEQLinkage job on Biowulf
back to top

Set up a batch script along the following lines:

# file called myjob.bat

module load seqlinkage 
seqlink --fam foo.fam --vcf bar.vcf.gz -f MERLIN -j 4 --tempdir /lscratch/$SLURM_JOB_ID

Submit this job with:

[user@biowulf ~]$ sbatch --cpus-per-task=4 --gres=lscratch:10 myjob.bat

For more information on submitting jobs to slurm, see Job Submission in the Biowulf User Guide.

Running a swarm of SEQLinkage jobs on Biowulf
back to top

Create a swarm command file like this sample

# --------file myjobs.swarm----------
seqlink --fam foo1.fam --vcf bar1.vcf.gz -f MERLIN
seqlink --fam foo2.fam --vcf bar2.vcf.gz -f MERLIN
seqlink --fam foo3.fam --vcf bar3.vcf.gz -f MERLIN
seqlink --fam fooN.fam --vcf barN.vcf.gz -f MERLIN
# -----------------------------------

Submit this set of runs to the batch system by typing

[user@biowulf ~]$ swarm --module seqlinkage -f myjobs.swarm

For details on using swarm see Swarm on Biowulf.

back to top