Joint-genotyping on terra

Post author
rezo mgeladze
Hello everyone!
I have several questions about Joint-genotyping workflow on terra:
 
 
1) Does the runtime environment create separate VM instances for each shard during importGVCF stage?
 
 
2) Do VM instances close automatically after I abort the workflow?
 
 
 
3) Does increasing CPU/Ram speed up the process of workflow?
Thanks! 

Comments

2 comments

  • Comment author
    Anika Das

    Hi Rezo, 

    Thanks for writing in with these questions! We will look into them and get back to you as soon as possible!

    Kind Regards, 

    Anika

    0
  • Comment author
    Anika Das

    Hi Rezo, 

    Please find the answers to your questions below:

    1) Does the runtime environment create separate VM instances for each shard during importGVCF stage?

    Yes, Google spins up a VM for each task and each shard.

    2) Do VM instances close automatically after I abort the workflow?
    Terra will send Google a request to stop and shutdown the VM instance when you abort the workflow in Terra.

    3) Does increasing CPU/Ram speed up the process of workflow?

    Yes increasing the CPU and memory typically speeds up the process of the workflow, though this is somewhat dependent on the tool and its ability to utilize the CPU and RAM effectively. Most tools benefit from an increase. See this excerpt from the article https://smallbusiness.chron.com/memory-affect-processors-70165.html:

    RAM not only allows your CPU to access files faster, it can also help your processor run more processes at the same time. The more RAM you have, and the faster the RAM cycles in MHz, the more processes your CPU can run.

    You can also consider increasing your disk size, as larger disks have higher I/O rates. See: https://cloud.google.com/compute/docs/disks/performance#performance_by_disk_size

     

    Hope that helps! Please let us know if you have any other questions!

    Kind Regards, 

    Anika

    0

Please sign in to leave a comment.