Trinity Performance - Runtime

CPU Usage Over Time

The Trinity pipeline consists of a series of executables, many of which run simultaneously. The charts below show the amount of CPU consumed by the individual processes over the course of a test run. The tests were performed on a single node with two eight-core processors for a total of 16 cores, and 500 gigabytes of memory.

Drosophila Data Set

Command line: Trinity --seqType fa --JM 20G --output ./trinity_out --CPU 32 --monitoring --left reads.left.fa --right reads.right.fa

Mouse Data Set

Command line: Trinity --seqType fa --max_memory 120G --SS_lib_type RF --bflyCalculateCPU --output trinity_out_Droso_2.1.1 --CPU 16 --monitoring --left reads.left.fa --right reads.right.fa

Pombe Data Set

The S. Pombe test consists of paired-end reads, including quality scores, with a length of 68.

Command line: Trinity --seqType fq --max_memory 120G --SS_lib_type RF --bflyCalculateCPU --output trinity_out_Schizo_2.1.1 --CPU 16 --monitoring --left reads.left.fq --right reads.right.fq