Open Danderson123 opened 6 days ago
This issue seems to come up fairly regularly so for anyone looking for a solution, mmseqs v14.7e284 worked on these sequences for me.
Killed
means that MMseqs2 didn't have enough RAM and was killed by the OOM killer.
I recommend to assign nodes exclusively to the MMseqs2 job, so another job can't steal the RAM.
Alternatively, you can use the --split-memory-parameter
to approximately set how much RAM MMseqs2 is allowed to use.
The parameter decides the size of the chunking with the prefilter, so it does not directly map to total RAM use. I recommend setting to. about 80% of the RAM you want to allow MMseqs2 to use.
So assuming you reserve 64GB RAM, you can pass --split-memory-limit 50G
to make MMseqs2 behave better with other software that require a lot of RAM.
Expected Behavior
mmseqs easy-cluster should finish without errors.
Current Behavior
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.
1) Download the FASTA at this link https://drive.google.com/file/d/1YPNMj2gL8zNUv9aiRo7dLJawanDWCIb3/view?usp=drive_link 2) Install mmseqs2 v15.6f452 3) Run:
MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
I am trying to cluster a number of gene sequences with an identity of 0.8 and no minimum length for the aligned portion of the genes.
Your Environment
Include as many relevant details about the environment you experienced the bug in.