When I run the fusion snakefile, the loose_gene_fusion file has >600K putative fusions. Then, the fusionfinder rule processes only 50 putative fusions consuming 500G memory and >20 hours of wall time.
Is this normal behaviour?
Since we have a strict memory reservation policy on the cluster, could you give me some suggestions on how I could speed up the pipeline，e.g. by setting strict parameters to the loose_fusions rule to cut down the number of putative fusions in loose_gene_fusion file?
Hi,
When I run the fusion snakefile, the loose_gene_fusion file has >600K putative fusions. Then, the fusionfinder rule processes only 50 putative fusions consuming 500G memory and >20 hours of wall time. Is this normal behaviour? Since we have a strict memory reservation policy on the cluster, could you give me some suggestions on how I could speed up the pipeline，e.g. by setting strict parameters to the loose_fusions rule to cut down the number of putative fusions in loose_gene_fusion file?