Anvi'o

Updated

Anvi'o versions 3, 4 and 5 are installed in their own environments within SCGC's anaconda3 package.

To load Anvi'o version 5 type:

module load anaconda3
source activate anvio5

To run it interactively, start an interactive session on charlie like so: (Note that by running "module purge" all other loaded software modules are also unloaded.)

julia at cfe1 in ~
$ qsub -I -q route -l walltime=8:00:00 -l ncpus=5,mem=32G -N anvio-interactive
qsub: waiting for job 33493.cfe1 to start
qsub: job 33493.cfe1 ready

julia at c1 in ~
$ module purge

julia at c1 in ~
$ module load anaconda3

julia at c1 in ~
$ source activate anvio5

From there you should be able to run any of the Anvi'o commands. e.g.:

(anvio5)
julia at c1 in ~
$ anvi-profile --version
Anvi'o version ...............................: 4
Profile DB version ...........................: 23
Contigs DB version ...........................: 10
Pan DB version ...............................: 8
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2

If you run a job submission using Anvi'o, make sure you have:

module purge
module load anaconda3
source activate anvio5

After your PBS parameters and before your terminal commands.

Interact with Anvio through your local browser:

Will need to open two terminals for this. The reference on the Anvi'o page is here, which we will follow with some tweaks: http://merenlab.org/2015/11/28/visualizing-from-a-server/

  1. In the first terminal, ssh into your account as normal, then start an interactive session:

qsub -I -q route -l walltime=0:80:00 -l ncpus=4,mem=4G -N <username>-interactive

  1. Load anvio
module use /mnt/scgc_nfs/opt/modulefiles/common
module load anaconda3
source activate anvio3

Could also load anvi'o 4, see github page on running anvio

  1. Navigate to the folder where your Anvi'o files are and run the interactive:
anvi-interactive -p SAMPLES-MERGED/PROFILE.db -c AM_ALLmeta_Norm_sccare.db --server-only -P 8099

Choose a different port number if that one is taken or not working. You should see a screen that says the server is now listening to the port.

  1. In second terminal: 
ssh -t -t username@cfe.bigelow.org -L 8099:localhost:8099 ssh c# -L 8099:localhost:8099

Replace username with your own user ID, c# with the charlie node that you are logged into (use chost to view node name) and whatever port you chose. You may see an error "bind: Cannot assign requested address" Ignore it. Do not close this terminal window.

  1. Go to any browser, and put in the address bar:

http://localhost:8099

(of course changing the ports to match above)

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