Stalling when zooming in

[Brendan Mullaney]

I have just installed IGV. When  I try and zoom in (even with no data) it stalls and doesn't respond. Why is this happening, they system should be able to handle it

[James Robinson]

Zoom into what level?  Fails to respond for how long?    If you are zooming into regions < 1kb or so it will query our servers for sequence data.   This is very quick for most people,  but if you have a poor network connection or firewalls blocking access it could be slow.  If that is the case the bests solution is to define your genome locally as described in the user guide.

Could you attach your igv.log file, located in an "igv" folder under your home directory?

On Fri, Dec 23, 2016 at 3:58 AM, Brendan Mullaney <brendan...@gmail.com> wrote:

I have just installed IGV. When  I try and zoom in (even with no data) it stalls and doesn't respond. Why is this happening, they system should be able to handle it

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[Brendan Mullaney]

It happens when I zoom in to <6KB level.

It seems to fail to respond indefinitely. I think you are correct it seems to be trying to retrieve sequence data. I have tried to down the hg19 genome but cant as its automatically in the genomes list. Wn I try and remove it and add form server it automatically come back into genome list when I click "more" so I cant tick the download sequence box. Is there a link to download the sequence manually and I can place it in the correct directory myself?

I have attached the log file.

On Friday, 23 December 2016 16:00:46 UTC, Jim Robinson wrote:

Zoom into what level?  Fails to respond for how long?    If you are zooming into regions < 1kb or so it will query our servers for sequence data.   This is very quick for most people,  but if you have a poor network connection or firewalls blocking access it could be slow.  If that is the case the bests solution is to define your genome locally as described in the user guide.

Could you attach your igv.log file, located in an "igv" folder under your home directory?

On Fri, Dec 23, 2016 at 3:58 AM, Brendan Mullaney <brendan...@gmail.com> wrote:

I have just installed IGV. When  I try and zoom in (even with no data) it stalls and doesn't respond. Why is this happening, they system should be able to handle it

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You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[Brendan Mullaney]

I have just tried to get it to download the genome but get the following errei

the log file is attached.

[James Robinson]

From this log it looks like you tried to run a binary file as a "batch" command.  

You can download the hg19 genome and fasta manually.  Download the following files, and keep them together in the igv/genomes directory.    If hg19 does not show up in the list manually add it from "Genomes > Load genome from file"  selecting the hg19.genome file.

https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.genome

https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta

https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai