Hi,
I am encountering an issue when trying to run BUSCO, which uses stats.sh to calculate contig/scaffold statistics of an input genome assembly. Unfortunately, for some large genomes/contigs, this causes stats.sh to fail when it exceeds the default maximum memory of 120 Mb.
BUSCO doesn't provide any control over the command-line arguments to be passed to bbtools, so I can't affect the memory allocation directly. Would it be possible to add functionality to javadetect.sh or memdetect.sh so that they could be overridden by setting environment variables, something like BBTOOLS_XMX?
Hi,
I am encountering an issue when trying to run BUSCO, which uses
stats.shto calculate contig/scaffold statistics of an input genome assembly. Unfortunately, for some large genomes/contigs, this causesstats.shto fail when it exceeds the default maximum memory of 120 Mb.BUSCO doesn't provide any control over the command-line arguments to be passed to bbtools, so I can't affect the memory allocation directly. Would it be possible to add functionality to
javadetect.shormemdetect.shso that they could be overridden by setting environment variables, something likeBBTOOLS_XMX?