I am using Galaxy to compare two whole-genome assemblies of alligator gar (Atractosteus spatula) as part of a male-versus-female genome comparison.
The two FASTA assemblies are:
- Reference / male: MaleAlligatorGar_fAtrSpa1.hap1_genomic.fna — approximately 1.17 GB
- Query / female: FemaleAlligatorGar_ASPAv1_genomic.fna — approximately 1.03 GB
I first aligned the genomes successfully using Minimap2 with the asm5 preset, and that whole-genome alignment completed without a problem.
I then attempted to generate a whole-genome structural comparison/dotplot using the Galaxy MUMmer dotplot tool with NUCmer. The NUCmer job failed because it exceeded the memory allocated to the job.
The failed outputs were:
- Dataset 19: NUCmer PDF — male vs. female alligator gar genomes
- Dataset 20: NUCmer PNG — male vs. female alligator gar genomes
Both report:
> “This job was terminated because it used more memory than it was allocated.”
Would it be possible to route this NUCmer/MUMmer job to a higher-memory compute destination on Galaxy?
If that is not available, could you recommend:
- another public Galaxy instance with more RAM for whole-genome NUCmer comparisons,
- a different Galaxy tool/configuration that would reduce memory usage,
- or an appropriate resource level for running this comparison externally?
These are chromosome-scale assemblies of the same species, approximately 1.0–1.2 Gb each. My goal is to examine large-scale synteny, inversions, rearrangements, and regions that differ between the male and female assemblies.
Thank you for any guidance you provide
