Unable to load mm9 genome

[prem pillai]

Hi there!

 

I am using IGV version 2.3.40 and in Windows 7.

It seems like for some reason I am not able to load the mm9 genome (though I am able to load the mm10).

I have attached the log report for the last session and the snapshot of the error message that I got.

Please advise me on this.

Thank you very much!

Kind regards,

Nisha.

 

[Jim Robinson]

Hi,

It looks like there was a network connection problem (timeout) before the mm9.genome file finished downloading.  I suggest removing it and starting over.   To do this select "Manage Genome List..." from the Genomes menu.  Find the Mouse mm9 entry, select, and click remove.   Then, to be sure, quite IGV and delete the "mm9.genome" file (if it exists) from your "igv/genomes" folder.    Restart igv and add it again.

Jim

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[prem pillai]

Hello Jim

thank you for this. As advised, i restarted IGV and reloaded the mm9 genome. I happen to encounter the same error.

Alternatively, i downloaded the genome directly using:

wget http://www.broadinstitute.org/igvdata/genomes/mm9.genome   

... and I find that the download fails (or freezes @99%) for this particular file. 

It works perfectly fine with other species that I randomly tried.

Kindly take a look at it and advise me on this.

Many thanks!

Best,

Nisha,

[Jim Robinson]

Hi,

I don't know what the issue could be, it downloads fine for me.   Here's an alternative URL to try.  Once downloaded you can load it directly with "Genomes > Load from file..."

http://igvdata.broadinstitute.org/genomes/mm9.genome

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[prem pillai]

Hia Jim,

Nope. your alternate link doesn't work either:: Snashot-download_incomplete.png shows this..

Also attached is the Error_ticket.txt that talks about a "read error" that happens at a particular point (which usually happens if the file is corrupt)

hmmm Tricky situation here,, since you are able to download it from your end..

Any other help or suggestion would be greatly appreciated.

If there is no way out, then I will use mm10 instead..

thank you for very much for your time with this.

Kind regards,

Nisha

[prem pillai]

Hey Jim! 

It works now. (Did a wget on that link you sent me)

Thank you once again for your time with this!

Best,

Nisha