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atavide_lite's Introduction

Edwards Lab License: MIT GitHub language count DOI

atavide lite

A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources

atavide is a full-fledged metagenome processing pipeline. This is a simpler version that uses either slurm scripts or PBS scripts to accomplish the same things. In this initial release, we avoided snakemake to work through the steps one at a time, although that will likely come soon.

See the verions:

  • slurm - designed to work on Flinders deepthought infrastructure
  • pbs - designed to work on the NCI infrastructrue for now

Currently the pipeline depends on these software

  • fastp
  • samtools
  • minimap2
  • megahit
  • mmseqs
  • vamb

You can install all of these with:

mamba env create -f ~/atavide_lite/atavide_lite.yaml

If you use atavide light, please cite it and then please also cite the other papers that describe these great tools.

atavide_lite's People

Contributors

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Stargazers

Michael Roach avatar Susie Grigson avatar

Watchers

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Forkers

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atavide_lite's Issues

VAMB issues

The VAMB version in the atavide_lite_vamb.yaml needs to be updated to 3.0.2 for use GPU computing. This update however might also create some issues with the current minimap/vamb implementation. The error when running vamb is a list of this error for each file:

[E::idx_find_and_load] Could not retrieve index file for 'vamb/mapped_reads/NFI_15tigershark_S7.bam'

When looking into the vamb scripts, two of the same minimap commands occur. Could this be causing the index file to be lost and throw this error?

vamb_minimap.slurm:

minimap2 -t 16 -N 5 -ax sr $BGFS/$OUTDIR/contigs.mmi --split-prefix $BGFS/mmsplit$$ $BGFS/fastq/$R1 $BGFS/fastq/$R2 | samtools view -F 3584 -b --threads 16 | samtools sort -@ 16 -o $BGFS/$OUTDIR/mapped_reads/$BAM -

vamb.slurm
minimap2 -t 16 -N 5 -ax sr $BGFS/$OUTDIR/contigs.mmi --split-prefix $BGFS/mmsplit$$ $BGFS/fastq/$R1 $BGFS/fastq/$R2 | samtools view -F 3584 -b --threads 16 | samtools sort -@ 16 -o $BGFS/$OUTDIR/mapped_reads/$BAM -

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