Anvi'o interactive does not load in Chrome browser

[celiosantosjr]

Anvi'o version ...............................: margaret (v5.1) Profile DB version ...........................: 29 Contigs DB version ...........................: 12 Pan DB version ...............................: 12 Genome data storage version ..................: 6 Auxiliary data storage version ...............: 2 Structure DB version .........................: 1

[celiosantosjr]

I tried to display the pangenome, but it just is loading for many days and no image was displayed. I use Ubuntu 16. Anvi'o was installed through virtual environment.

Interactive mode .............................: pan                                                                      
Genomes storage .............................................: Initialized (storage hash: hash95c35d6a)                  
Num genomes in storage ......................................: 45
Num genomes will be used ....................................: 45
Pan DB ......................................................: Initialized: ROKUBACTERIA_Pan-PAN.db (v. 12)

* Gene clusters are initialized for all 22082 gene clusters in the database.

WARNING
==============================================================
Genomes storage does not have any info about gene functions. Certain parts of
the pangenomic workflow will not be accessible.

* The server is now listening the port number "8080". When you are finished, press
CTRL+C to terminate the server.```

[ozcan]

Is this a personal computer or server environment? it seems anvi'o interactive is listening on port 8080 without any problem, Can you access localhost:8080 or 127.0.0.1:8080 on your browser? Sometimes everything works but it just does not pop up for some reason.

If this is is running on a server you need ssh tunneling to browse it, below some links related to that.

http://merenlab.org/2015/11/28/visualizing-from-a-server/ http://merenlab.org/2018/03/07/working-with-remote-interative/

[celiosantosjr]

Hi,

This is a personal computer. Actually, still does not work, but now i have some error messages.

Interactive mode .............................: pan                             
Genomes storage .............................................: Initialized (storage hash: hash95c35d6a)
Num genomes in storage ......................................: 45
Num genomes will be used ....................................: 45
Pan DB ......................................................: Initialized: ROKUBACTERIA_Pan-PAN.db (v. 12)

* Gene clusters are initialized for all 22082 gene clusters in the database.

WARNING
==============================================================
Genomes storage does not have any info about gene functions. Certain parts of
the pangenomic workflow will not be accessible.

* The server is now listening the port number "8080". When you are finished, press
CTRL+C to terminate the server.
[1:1:0926/111144.335430:ERROR:webthread_impl_for_utility_thread.cc(19)] Not implemented reached in virtual blink::ThreadScheduler *blink::scheduler::WebThreadImplForUtilityThread::Scheduler() const
[1:1:0926/111240.636601:ERROR:webthread_impl_for_utility_thread.cc(19)] Not implemented reached in virtual blink::ThreadScheduler *blink::scheduler::WebThreadImplForUtilityThread::Scheduler() const
[1:1:0926/111607.763005:ERROR:webthread_impl_for_utility_thread.cc(19)] Not implemented reached in virtual blink::ThreadScheduler *blink::scheduler::WebThreadImplForUtilityThread::Scheduler() const
[1:1:0926/111607.943615:ERROR:webthread_impl_for_utility_thread.cc(19)] Not implemented reached in virtual blink::ThreadScheduler *blink::scheduler::WebThreadImplForUtilityThread::Scheduler() const

[ozcan]

This kind of errors appears sometime, related to Chrome. But when you open browser by yourself can you browse 127.0.0.1:8080?

[celiosantosjr]

I got this message:

This site can’t be reached
127.0.0.1 refused to connect.
Try:

Checking the connection
Checking the proxy and the firewall
ERR_CONNECTION_REFUSED

[ozcan]

Do you see the message below in the terminal when you try this?

* The server is now listening the port number "8080". When you are finished, press
CTRL+C to terminate the server.```

[celiosantosjr]

Yes, i did

[ozcan]

Sorry for the inconvenience, this seems really interesting. Can you try adding flags below when running anvi-display-pan

--server-only --ip-address 127.0.0.1

Then after seeing message

* The server is now listening the port number "8080". When you are finished, press
CTRL+C to terminate the server.

You should be able to open any browser and browse 127.0.0.1:8080

[meren]

I assume this is addressed since it's been three days we haven't heard from @celiosantosjr :)