System resources usage¶

Generating current differences¶

nanodisco preprocess

This command performs sequencing reads extraction from the fast5, and then mapping fasta on the reference genome.
A typical runtime is ~40 min with 20 threads for a 5.5 Mb genome sequenced at 140x (~3 GB memory used).

nanodisco difference

A typical runtime is ~16 min with 4 threads (2 jobs with 2 threads each) for 10 chunks at sequencing depth of ~85x (~10 GB memory used).
The computation of current differences can be optimized by using -nj to use maximum available computing resources.
HPC infrastructure can also be leverage by starting jobs on multiple nodes using -f and -l to specify unique chunk ranges. Recommendation for users with HPC access can be found in the FAQ.

nanodisco motif

A typical runtime for the detection of 4 motifs from a 4.5 Mb genome is ~20 min with 4 threads.
Runtime generally depends on the genome size and the number of methylation motifs.

nanodisco characterize

A typical runtime for the characterization of 4 motifs is ~7 min with 4 threads (~10 GB memory used).
Runtime generally depends on the genome size, the number of input methylation motifs, and the number of occurrences.

nanodisco profile (motif-guided)

A typical runtime for the profiling of 60 motifs in a 90 Mb metagenome is ~3 min with 20 threads (~140 GB of memory used).
Runtime generally depends on the number of input motifs and the metagenome size.

nanodisco profile (automated)

A typical runtime for the profiling of all common motifs in a 90 Mb metagenome is ~41 hours with 20 threads (>240 GB of memory used).
Runtime generally depends on the metagenome size (contigs longer than 100 kb by default).

nanodisco select_feature

A typical runtime is ~45 min with 4 threads (~140 GB of memory used).
Runtime generally depends on the diversity of methylation motifs in the microbiome and the metagenome size.

nanodisco filter_profile

A typical runtime for the profiling of 3769 methylation features in a 90 Mb metagenome is ~25 min with 20 threads (>240 GB of memory used).
Runtime generally depends on the diversity of methylation motifs in the microbiome and the metagenome size.

N.B.

All tests were performed on an Intel(R) Xeon(R) Platinum 8168 CPU @ 2.70GHz.