Trinity Example Files

{loadposition example-job-caution}

Run Trinity in one step

This example runs all stages of Trinity in one step. This is only advised for small datasets — datasets that require a maximum of 16 cores or 128 Gb of memory, and that are expected to completely finish within 96 hours.

Files include:

reads.left.fq.gz, input data
reads.right.fq.gz, input data
trinity_all.job, PBS script	View
trinity_all.log, trinity output and error	View
trinity_all.output, PBS standard output and error	View

Run Trinity in multiple steps

Running Trinity in multiple steps is recommended for large datasets. If a job requires more than 96 hours to complete, PSC User Services can extend the time. To request a time extension, please contact User Services as soon as you know that it is necessary.

These jobs break the Trinity run into four steps:

Stage 1 – generate the kmer-catalog and runs Inchworm
Stage 2 – do the Chrysalis clustering of Inchworm contigs and mapping reads
Stage 3 – conduct the Chrysalis deBruijn graph construction
Stage 4 – run Butterfly and generate the final Trinity.fasta file

To run Trinity this way, submit the job for stage 1 (trinity_stage1.job). When it completes sucessfully, submit the second job, trinity_stage2.job, and so on.

Files include:

Stage 1: generate the kmer-catalog and run Inchworm

reads.left.fq.gz, input data
reads.right.fq.gz, input data
trinity_stage1.job, PBS script	View
trinity_stage1_example.log, trinity output and error	View
trinity_stage1.output, PBS standard output and error	View

Stage 2: do Chrysalis clustering of Inchworm contigs and mapping reads

trinity_stage2.job, PBS script	View
trinity_stage2_example.log, trinity output and error	View
trinity_stage2.output, PBS standard output and error	View

Stage 3: construct the Chrysalis deBruijn graphs

trinity_stage3.job, PBS script	View
trinity_stage3_example.log, trinity output and error	View
trinity_stage3.output, PBS standard output and error	View

Stage 4: run Butterfly and generate the final Trinity.fasta file

trinity_stage4.job, PBS script	View
trinity_stage4_example.log, trinity output and error	View
trinity_stage4.output, PBS standard output and error	View

Big assemblies scripts

This job script shows how to run Trinty with big assemblies: those with more than 200 million reads or those that use more than 64 cores.

big_assemblies.job, PBS script	View

Trinity example files