Squeezemeta

Introduction

SqueezeMeta is a fully automated metagenomics pipeline, from reads to bins.

For more information, please check:
Home page: https://github.com/jtamames/SqueezeMeta

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.5.1

BELL

1.5.1

GAUTSCHI

1.5.1

NEGISHI

1.5.1

SCHOLAR

1.5.1

Commands

  • 01.merge_assemblies.pl

  • 01.merge_sequential.pl

  • 01.remap.pl

  • 01.run_assembly.pl

  • 01.run_assembly_merged.pl

  • 02.rnas.pl

  • 03.run_prodigal.pl

  • 04.rundiamond.pl

  • 05.run_hmmer.pl

  • 06.lca.pl

  • 07.fun3assign.pl

  • 08.blastx.pl

  • 09.summarycontigs3.pl

  • 10.mapsamples.pl

  • 11.mcount.pl

  • 12.funcover.pl

  • 13.mergeannot2.pl

  • 14.runbinning.pl

  • 15.dastool.pl

  • 16.addtax2.pl

  • 17.checkM_batch.pl

  • 18.getbins.pl

  • 19.getcontigs.pl

  • 20.minpath.pl

  • 21.stats.pl

  • SqueezeMeta.pl

  • SqueezeMeta_conf.pl

  • SqueezeMeta_conf_original.pl

  • parameters.pl

  • restart.pl

  • add_database.pl

  • cover.pl

  • sqm2ipath.pl

  • sqm2itol.pl

  • sqm2keggplots.pl

  • sqm2pavian.pl

  • sqm_annot.pl

  • sqm_hmm_reads.pl

  • sqm_longreads.pl

  • sqm_mapper.pl

  • sqm_reads.pl

  • versionchange.pl

  • find_missing_markers.pl

  • remove_duplicate_markers.pl

  • anvi-filter-sqm.py

  • anvi-load-sqm.py

  • sqm2anvio.pl

  • configure_nodb.pl

  • configure_nodb_alt.pl

  • download_databases.pl

  • make_databases.pl

  • make_databases_alt.pl

  • test_install.pl

Module

You can load the modules by:

module load biocontainers
module load squeezemeta

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run squeezemeta on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers squeezemeta

# Your squeezemeta workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers squeezemeta

# Your squeezemeta workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers squeezemeta

# Your squeezemeta workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers squeezemeta

# Your squeezemeta workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=squeezemeta
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers squeezemeta

# Your squeezemeta workflow...