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Maintenance: Tues, 28 Jan 2020


Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
User Portal                   8:00am to 5:00pm MST
The User Portal,, will be unavailable while we perform maintenance and updates.
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA 

Keep up to date with our maintenance schedules on the CyVerse public calendar
Check your local timezone here 
Please contact for any questions, or concerns.






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To log in to the Atmosphere virtual machine, do the following:

  1. Go to www.
  2. Log in using your iPlant CyVerse credentials.
  3. After clicking launch New Instance, look for STACKS Ubuntu 16 Stacks 1.23 v146 v.2.0, and then select it.
  4. Under instance type, select tiny2.
  5. Click Launch Instance.


Note: All staged data we will be using for this exercise are under /home/<your_cyverse_username>/stacks_demo.

  1. Connect to the Atmosphere image. (Detailed instructions are located here
  2. From the command line use “mkdir” to create a folder were we will work and save our work):
    cd ~
    mkdir ~/stacks_demo
  3. After that use “cd” command to move into the newly created directory.
    cd stacks_demo

Clean and demultiplex the data


  1. Within the stacks_demo directory, create a subdirectory called “demultiplex_samples” by using:
    mkdir demuplix_samples
  2. From the stacks_demo directory, execute the following command:
    process_radtags -p ~/home/stacks_demo/fastq_files/ -o ~/stacks_demo/demultiplex_samples/ -b ~/stacks_demo/61VBPAAXX_key.txt -e apeKI -r -c --q