Anvi'o-Sapelo2

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Category

Bioinformatics

Program On

Sapelo2

Version

4, 5.1, 5.3, 5.4, 6.1, 7, 7.1

Author / Distributor

Please see http://merenlab.org/software/

Description

From http://merenlab.org/software/anvio: "Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.

It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs."

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo2 please see the Lmod page.

  • Version 4 is installed as a singularity image at /apps/singularity-images/anvio-4.simg
  • Version 5.1 is installed as a singularity image at /apps/singularity-images/anvio-5.1.simg
  • Version 5.3 is installed as a singularity image at /apps/singularity-images/anvio-5.3.simg
  • Version 5.4 is installed as a singularity image at /apps/singularity-images/anvio-5.4.simg
  • Version 6.1 is installed as a singularity image at /apps/singularity-images/anvio-6.1.simg
  • Version 7 is installed as a singularity image at /apps/singularity-images/anvio-7.simg
  • Version 7.1 is installed as a conda environment in /apps/gb/anvio/7.1


To check all the programs included in the singularity image version 5.1: 

singularity exec /apps/singularity-images/anvio-5.1.simg  ls /usr/local/bin

To check all the programs included in the singularity image version 6.1: 

singularity exec /usr/local/singularity-images/anvio-6.1.simg ls /opt/conda/envs/anvioenv/bin


To check the version of the anvio programs in the singularity image: 

singularity exec /usr/local/singularity-images/anvio-6.1.simg anvi-profile --version
Anvi'o version ...............................: esther (v6.1)
Profile DB version ...........................: 31
Contigs DB version ...........................: 14
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1

singularity exec /apps/singularity-images/anvio-7.simg  anvi-profile --version
Anvi'o .......................................: hope (v7)
Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1

To run v. 7.1, please first load the anvio/7.1_conda module and then activate the conda environment. This example first starts an interactive session: 

[shtsai@ss-sub1 ~] interact

[shtsai@b1-24 ~] ml anvio/7.1_conda

[shtsai@b1-24 ~] source activate $EBROOTANVIO
(/apps/gb/anvio/7.1) [shtsai@b1-24 ~]$ anvi-profile --version
Anvi'o .......................................: hope (v7.1)

Profile database .............................: 38
Contigs database .............................: 20
Pan database .................................: 15
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 2

(/apps/gb/anvio/7.1) [shtsai@b1-24 ~]$ conda deactivate
[shtsai@b1-24 ~]$


Sample job submission script (sub.sh) to run anvi-profile version 6.1: 

#!/bin/bash
#SBATCH --job-name=testanvio          # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=5gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR

singularity exec /apps/singularity-images/anvio-6.1.simg anvi-profile [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.


Sample job submission script (sub.sh) to run anvi-profile version 7.1: 

#!/bin/bash
#SBATCH --job-name=testanvio          # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=5gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR
ml anvio/7.1_conda
source activate $EBROOTANVIO
anvi-profile [options]
conda deactivate

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with 

sbatch sub.sh

Documentation

Please see http://merenlab.org/software/anvio/

Installation

Singularity images built from the docker container provided by the authors. For example:

singularity pull docker://meren/anvio

The conda environment for v. 7.1 was installed using Miniconda3/4.10.3 and Python 3.6.

System

64-bit Linux

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