--cores
option sets the maximum number of cores to use. The default value is 1. When running in cluster mode, this restricts the number of cores per job submitted.--local-cores
option sets the maximum number of cores to use on local rules when running in cluster mode. The default value is 1.--cluster-retries
option sets the number of times to retry a failed job. The default value is 3. This is especially important when using --run-aviary
to run assembly and genome recovery. Jobs are submitted with sequentially increasing walltime, and sometimes CPUs and RAM with each failure. See below.If you encounter memory issues with target_elusive or cluster_graph, you can try the following:
--kmer-precluster
option can be set to always
to enable kmer preclustering. This is the default if more than 1000 samples are provided. This greatly reduces memory usage and allows scaling up to at least 250k samples on a single HPC node. Kmer preclustering can be disabled with --kmer-precluster never
.--precluster-size
option sets the maximum number of samples to use for preclustering. The default value is 5 x the number of recovery samples. Reducing this value will reduce memory usage by reducing the number of combinations that are considered. However, this reduces the samples combinations that are considered for both coassembly and differential-abundance binning (co-binning), so may result in sub-optimal coassembly suggestions.--taxa-of-interest
option can be used to filter the taxa of the considered sequences to target a specific taxon. This can reduce memory usage.Snakemake profiles can be used to automatically submit jobs to HPC clusters (--snakemake-profile
).
Note that Aviary assemble commands are submitted to the cluster, while Aviary recover commands are run locally such that Aviary handles cluster submission.
The --cluster-submission
flag sets the local Aviary recover thread usage to 1, to enable multiple runs in parallel by setting --local-cores
to greater than 1.
This is required to prevent --local-cores
from limiting the number of threads per submitted job.
--aviary-assemble-cores
option sets the maximum number of cores for Aviary assemble to use. The default value is 64.--aviary-assemble-memory
option sets the maximum amount of memory for Aviary assemble to use (in Gigabytes). The default value is 500.--assembly-strategy dynamic
(default) option means that assembly is initially attempted using metaSPAdes with 32 CPUs, 250 GB RAM. If this fails, metaSPAdes is attempted again with 64 CPUs, 500 GB RAM. If this also fails, MEGAHIT is attempted with 32 CPUs, 250 GB RAM.--assembly-strategy metaspades
option means that assembly is attempted using metaSPAdes with 32 CPUs, 250 GB RAM, with CPUs and RAM increasing with each attempt.--assembly-strategy megahit
option means that assembly is attempted using MEGAHIT with 32 CPUs, 250 GB RAM, with CPUs and RAM increasing with each attempt.--aviary-recover-cores
option sets the maximum number of cores for Aviary recover to use. The default value is 32. If --cluster-submission
is set, then this applies to jobs submitted by Aviary. Binners, refinement steps and characterisation are submitted as separate jobs.--aviary-recover-memory
option sets the maximum amount of memory for Aviary recover to use (in Gigabytes). The default value is 250. If --cluster-submission
is set, then this applies to jobs submitted by Aviary.Powered by Doctave