Comments (1)
tseemann
commented on September 24, 2024
@rec3141 i never anticipated this be used for a 100 Mbp genome. My focus is bacterial genomes.
I recently added a --ram option that gets used for Spades and KMC (default 32 GB max). You will need to get the latest Shovill 0.5.1 off github directly (clone).
However I use the Pilon wrapper script which sets the RAM inside it (I think I made it 8G). I believe I (and your) might be able to do export _JAVA_OPTIONS="-Xmx48g" before running it.
I have made this change in bcb8fb0 (version 0.6.0). Let me know if it works for you!
shovill --ram 48 --outdir XXX --R1 XXX --R2 XXX
PS. Are you using Spades 3.10? It claims lower memory usage than previous versions.
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Related Issues (20)
- Pilon memory config error
- [shovill] Assembly failed - spades.fasta has zero contigs! HOT 1
- Resulting contig is way longer than expected
- Spades finished abnormally, OS return value: 21
- Error
- Error 256 HOT 2
- Confusing min ram requirements
- Failed to download resource "velvet"
- Coverage information for contigs assembled by Megahit
- Shovil tool on genome assembly of staph MRSA has 5632 error
- Harishk illumina sequence
- Hsrish
- Error 256 HOT 3
- GFA files in skesa
- what fastq filetype are available to use shovill ?
- Running shovill 1.1.0 and passing the option `'--plasmid'` to spades HOT 2
- [shovill] Can't see adapter file: /usr/local/db/trimmomatic.fa
- Illegal division by zero at /usr/local/bin/shovill line 162.
- Does Shovill support bash for running multiple fastq input files
- is it going to be compatible with SPAdes v4.0
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