how_to_kill_trinity
If you need to kill the Trinity process for any reason and it's during phase-2, it can be a challenge, because it will retry sub-jobs automatically in case there was a hiccup of some sort (usually involving the file system or resources not keeping pace). To get around this, you need to be able to kill the parent process that's spawning the sub-jobs.
To find the parent process, you can run:
ps axjf
and search for the parent Trinity job at the top of the Trinity job tree.
Once you have that process ID, you can run:
kill -9 $pid
the ParaFly process is responsible for managing the phase-2 Trinity jobs. In phase-2, if a Trinity sub-job fails, it will retry it a handful of times automatically to ensure its a true failure and not something sporadic. If you can kill this ParaFly parent process (highlighted above in red), that should end the phase-2 execution.
Another much easier way to do it is to try to kill all jobs that have Trinity or ParaFly in the name, which can be done like so (as a last resort):
ps auxww | egrep "Trinity|ParaFly" | grep -v grep | awk '{ print $2;}' | xargs -n1 -I {} kill -9 {}
- 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