pangenome on Biowulf

From the pangenome user manual:

nf-core/pangenome is a bioinformatics best-practise analysis pipeline for the rendering of a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs.
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

Allocate an interactive session with sinteractive and use as shown below. In this case we will use test data that is an artificial mixture of 1M human exome reads and 1M environmental metagenomic reads. The 50% human reads is treated as an artificial contamination and removed:

[user@biowulf]$ sinteractive --mem=36g --cpus-per-task=12 --gres=lscratch:10
salloc.exe: Pending job allocation 33247354
salloc.exe: job 33247354 queued and waiting for resources
salloc.exe: job 33247354 has been allocated resources
salloc.exe: Granted job allocation 33247354
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@nc3144]$ module load pangenome
[user@nc3144]$ cd /lscratch/${SLURM_JOB_ID}
[user@nc3144]$ vg
vg: variation graph tool, version v1.40.0 "Suardi"

usage: /usr/local/bin/vg  [options]

main mapping and calling pipeline:
  -- autoindex     mapping tool-oriented index construction from interchange formats
  -- construct     graph construction
  -- rna           construct splicing graphs and pantranscriptomes
  -- index         index graphs or alignments for random access or mapping
  -- map           MEM-based read alignment
  -- giraffe       fast haplotype-aware short read alignment
  -- mpmap         splice-aware multipath alignment of short reads
  -- augment       augment a graph from an alignment
  -- pack          convert alignments to a compact coverage index
  -- call          call or genotype VCF variants
  -- help          show all subcommands

For more commands, type `vg help`.
For technical support, please visit:

[user@nc3144]$ pggb
[user@nc3144]$ odgi
odgi: optimized dynamic genome/graph implementation, version v0.8.3-0-g34f006f3

usage: /usr/local/bin/odgi  [options]

Overview of available commands:
  -- bin           Binning of pangenome sequence and path information in the graph.
  -- break         Break cycles in the graph and drop its paths.
  -- build         Construct a dynamic succinct variation graph in ODGI format from a GFAv1.
  -- chop          Divide nodes into smaller pieces preserving node topology and order.
  -- cover         Cover the graph with paths.
  -- crush         Crush runs of N.
  -- degree        Describe the graph in terms of node degree.
  -- depth         Find the depth of a graph as defined by query criteria.
  -- draw          Draw previously-determined 2D layouts of the graph with diverse annotations.
  -- explode       Breaks a graph into connected components storing each component in its own file.
  -- extract       Extract subgraphs or parts of a graph defined by query criteria.
  -- flatten       Generate linearizations of a graph.
  -- flip          Flip path orientations to match the graph.
  -- groom         Harmonize node orientations.
  -- heaps         Path pangenome coverage permutations.
  -- inject        Inject BED annotations as paths.
  -- kmers         Display and characterize the kmer space of a graph.
  -- layout        Establish 2D layouts of the graph using path-guided stochastic gradient descent.
  -- matrix        Write the graph topology in sparse matrix format.
  -- normalize     Compact unitigs and simplify redundant furcations.
  -- overlap       Find the paths touched by given input paths.
  -- panpos        Get the pangenome position of a given path and nucleotide position (1-based).
  -- pathindex     Create a path index for a given graph.
  -- paths         Interrogate the embedded paths of a graph.
  -- pav           Presence/absence variants (PAVs).
  -- position      Find, translate, and liftover graph and path positions between graphs.
  -- priv          Differentially private sampling of graph subpaths.
  -- procbed       Procrustes-BED: adjust BED to match subpaths in graph.
  -- prune         Remove parts of the graph.
  -- server        Start a basic HTTP server to lift coordinates between path and pangenomic positions.
  -- similarity    Provides a sparse similarity matrix for paths or groups of paths.
  -- sort          Apply different kind of sorting algorithms to a graph.
  -- squeeze       Squeezes multiple graphs in ODGI format into the same file in ODGI format.
  -- stats         Metrics describing a variation graph and its path relationship.
  -- stepindex     Generate a step index and access the position of each step of each path once.
  -- tension       evaluate the tension of a graph helping to locate structural variants and abnormalities
  -- tips          Identifying break point positions relative to given references.
  -- unchop        Merge unitigs into a single node preserving the node order.
  -- unitig        Output unitigs of the graph.
  -- untangle      Project paths into reference-relative, to decompose paralogy relationships.
  -- validate      Validate a graph checking if the paths are consistent with the graph topology.
  -- version       Print the version of ODGI to stdout.
  -- view          Project a graph into other formats.
  -- viz           Visualize a variation graph in 1D.

[user@nc3144]$ # copy test data
[user@nc3144]$ cp $PANGENOME_TEST_DATA/* .
[user@nc3144]$ cp /usr/local/apps/nextflow/nextflow.config .
[user@nc3144]$ # run pangenome on the test data with biowulflocal profile
[user@nc3144]$ nextflow run nf-core/pangenome \
-r dev -profile biowulflocal \
--input DRB1-3123.fa.gz \
--n_haplotypes 12 \
--outdir testout \
-with-singularity  $PANGENOME_PATH/pangenome.img
[user@nc3144]$ exit

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. similar to the following example:

#! /bin/bash

module load pangenome || exit 1

if [[ ! -e DRB1-3123.fa.gz ]]; then
cp /usr/local/apps/nextflow/nextflow.config .

nextflow run nf-core/pangenome \
-r 1.0.0 -profile biowulf \
--input DRB1-3123.fa.gz \
--n_haplotypes 12 \
--outdir testout \
-with-singularity  $PANGENOME_PATH/pangenome.img

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=12 --mem=72g --gres=lscratch:10