graphaligner on Biowulf

Seed-and-extend program for aligning long error-prone reads to genome graphs.


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 --cpus-per-task=2 --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]$ module load graphaligner
[user@cn3144]$ cp -r ${GRAPHALIGNER_TEST_DATA:-none} test
[user@cn3144]$ GraphAligner -t $SLURM_CPUS_PER_TASK -g test/graph.gfa -f test/read.fa -a test/aln.gaf -x vg
[user@cn3144]$ cat test/aln.gaf
read    71      0       71      +       >1>2>4  87      3       73      67      72      60      NM:i:5  AS:f:56.3       dv:f:0.0694444  id:f:0.930556   cg:Z:4=1X2=1I38=1D5=1I5=1X13=

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

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g., which uses the input file ''. For example:

module load graphaligner/1.0.16
    -f $GRAPHALIGNER_TEST_DATA/read.fa -a aln.gaf -x vg

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2
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. graphaligner.swarm). For example:

GraphAligner -g input1/graph.gfa -t $SLURM_CPUS_PER_TASK -f input1/read.fa -a output1/aln.gaf -x vg
GraphAligner -g input2/graph.gfa -t $SLURM_CPUS_PER_TASK -f input2/read.fa -a output2/aln.gaf -x vg

Submit this job using the swarm command.

swarm -f graphaligner.swarm -g 4 -t 2 --module graphaligner/1.0.16
-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 graphaligner Loads the graphaligner module for each subjob in the swarm