AssemblyHaplotypesMultiThreadPlugin fails

Question

[kathrynm]

Hello,

I am trying to run the AssemblyHaplotypesMultiThreadPlugin from a docker container and the job keeps failing after about four-six hours. I am using 80 out of 124 GB of memory and 10 out of 24 threads, and there are no error messages or "killed" statements. I removed the initial assembly where the job was failing, but that didn't fix the issue.

I am currently trying to use both the NAM genomes and our 5 stiff stalk genomes, they all have uniform headers for the fastas. I reran PHG using just the 5 stiff stalks (as I have done previously), and it worked then.

Thoughts? Thanks, Kathryn

Answer 1

[lcj34]

Kathryn - can you post the log file that was run? Or send to me directly? ([e-mail])

[lcj34]

Kathryn - When you say "failing" - does the job quit or does it hang? Again, the log file may help.