AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[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 AMOS [user@cn3144 ~]$ AMOScmp -D "TGT=mytarget.afg" -D "REF=myreference.1con" prefix [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. AMOS.sh). For example:
#!/bin/bash set -e module load AMOS AMOScmp -D "TGT=mytarget.afg" -D "REF=myreference.1con" prefix
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] AMOS.sh