Difference between revisions of "Applications/guppy"
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===Calculate assembly contiguity statistics=== | ===Calculate assembly contiguity statistics=== | ||
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[username@login] module load abyss/1.5.2/gcc-4.9.3 | [username@login] module load abyss/1.5.2/gcc-4.9.3 | ||
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The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page. | The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page. | ||
| − | Do not run mpirun -np 8 abyss-pe. To run ABySS with 8 threads, use abyss-pe np=8. The abyss-pe driver script will start the MPI process, like so: mpirun -np 8 ABYSS-P. | + | Do not run '''mpirun -np 8 abyss-pe'''. To run ABySS with 8 threads, use '''abyss-pe np=8'''. The abyss-pe driver script will start the MPI process, like so: '''mpirun -np 8 ABYSS-P.''' |
The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np. | The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np. | ||
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#SBATCH -N 2 | #SBATCH -N 2 | ||
#SBATCH --ntasks-per-node=40 | #SBATCH --ntasks-per-node=40 | ||
| + | #SBATCH -o %N.%j.%a.out | ||
| + | #SBATCH -e %N.%j.%a.err | ||
| + | #SBATCH --exclusive | ||
#SBATCH -t 00:30:00 | #SBATCH -t 00:30:00 | ||
Revision as of 15:06, 3 April 2017
Contents
Application Details
- Description: ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
- Version: 1.5.2 (gcc-4.9.3)
- Modules: abyss/1.5.2/gcc-4.9.3
- Licence: Free, open-source
Usage Examples
Assemble a small synthetic data set
[username@login] module load abyss/1.5.2/gcc-4.9.3
[username@login] wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz
[username@login] tar xzvf test-data.tar.gz
[username@login} abyss-pe k=25 name=test \
in='test-data/reads1.fastq test-data/reads2.fastq'
Calculate assembly contiguity statistics
[username@login] module load abyss/1.5.2/gcc-4.9.3 [username@login] abyss-fac test-unitigs.fa
Parallel processing
The np option of abyss-pe specifies the number of processes to use for the parallel MPI job. Without any MPI configuration, this will allow you to use multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is described in the mpirun man page.
Do not run mpirun -np 8 abyss-pe. To run ABySS with 8 threads, use abyss-pe np=8. The abyss-pe driver script will start the MPI process, like so: mpirun -np 8 ABYSS-P.
The paired-end assembly stage is multithreaded, but must run on a single machine. The number of threads to use may be specified with the parameter j. The default value for j is the value of np.
Note: this example is done on a high memory node, usually access would be achieved with the scheduler
[username@c230 ~]$ module add abyss/1.5.2/gcc-4.9.3 [username@c230 ~]$ mpirun abyss-pe np=40
Through SLURM this would become the script:
#!/bin/bash #SBATCH -J abyss #SBATCH -p highmem #SBATCH -N 2 #SBATCH --ntasks-per-node=40 #SBATCH -o %N.%j.%a.out #SBATCH -e %N.%j.%a.err #SBATCH --exclusive #SBATCH -t 00:30:00 module purge module load abyss/1.5.2/gcc-4.9.3 #Run your ABySS commands abyss-pe name=test k=48 n=8 in='test-1.fa test-3.fa'