Hey Anvio Team!
I have been using Anvio on our server and I have recently made 109 bins with CONCOCT. I need to refine a few of them and am planning on doing this with Anvio. I unfortunately can not open anvi-interactive/anvi-refine using our server. This is the command and the error that I recieve:
$ anvi-interactive -c 02_Contigs_Bac/Bac_contigs.db -p 04_Profile_Bac/Bac_Profile/PROFILE.db
Contigs DB ...................................: Initialized: 02_Contigs_Bac/Bac_contigs.db (v. 14)
Interactive mode .............................: full
Auxiliary Data ...............................: Found: 04_Profile_Bac/Bac_Profile/AUXILIARY-DATA.db (v. 2)
Profile Super ................................: Initialized with all 56440 splits: 04_Profile_Bac/Bac_Profile/PROFILE.db (v. 31)
Looking up 0.0.0.0:8080
Making HTTP connection to 0.0.0.0:8080
Alert!: Unable to connect to remote host.
lynx: Can't access startfile http://0.0.0.0:8080/
* The server is now listening the port number "8080". When you are finished, press
CTRL+C to terminate the server.
I have since tried to see if I could just use the docker container to run this from my own computer. I have followed this turtorial:
The download went well and everything seems to be as it should for the docker container. Yet when I run the below command within the directory my files are I get the below error:
$docker run --rm -it -v 'pwd':'pwd' -w 'pwd' -p 8080:8080 meren/anvio:latestdocker: Error response from daemon: the working directory ''pwd'' is invalid, it needs to be an absolute path.
See 'docker run --help'.
I have also tried to type in the full path but I get the same error (instead of 'pwd' it is the full path I typed in). Do you have any suggestions for what I may be doing wrong.
Also, I am currently using Anvio version 6.1. I am working with our IT team to get anvio v7 installed on the server but for now I only have the 6.1 available on the server. Yet now I can use v7 with the docker if I get it working. :)
Thanks again!
Hannah