Trinity Progress Monitoring
#Monitoring the Progress of Trinity
Since Trinity can easily take several days to complete a large trancriptome assembly job, it is useful to be able to monitor the process and to know at which stage (Inchworm, Chrysalis, Butterfly) Trinity is currently at. There are a few general ways to do this:
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by running 'top', you'll be able to see which Trinity process is running and how much memory is being consumed.
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other downstream process will generate standard output. Be sure to capture 'stdout' and 'stderr' when you run the Trinity script. The format for capturing both stdout and stderr depends on your SHELL. Figure out what shell you have by running:
env | grep SHELL
Using tcsh:
Trinity ... opts ... > & run.log &
Using bash:
Trinity ... opts ... > run.log 2>&1 &
Note, under bash, to prevent the background process from being terminated once you close the shell, type 'exit' to leave the shell, or explore alternatives such as nohup, disown, or screen.
You can then 'tail -f run.log' to follow the progress of the Trinity throughout the various stages.
- Trinity Wiki Home
- Installing Trinity
- Running Trinity
- Trinity process and resource monitoring
- Output of Trinity Assembly
- Assembly Quality Assessment
- Downstream Analyses
- Miscellaneous additional functionality that may be of interest
- Contributing code
- Trinity Tidbits
- Frequently Asked Questions (FAQ)
- There are too many transcripts! What do I do?
- How to minimize RAM usage
- How do I use reads I downloaded from SRA
- How do I identify the specific reads that were incorporated into the transcript assemblies?
- How can I perform cross-species analysis?
- How do I combine PE and SE reads?
- How can I run this in parallel on a computing grid?
- Computing and Time requirements
- Errors during Trinity run
- Killing Trinity
- Contact us