Error loading genome

[shom...@gmail.com]

Hello

I am using IGV 2_4.18 on a Mac (High Sierra 10.13.6) and Java 8. Have always had no issues with IGV. For last few days, every time I open IGV it says "loading genome" for a long time and eventually gives an error message. 

Any ideas on how to fix this would be greatly appreciated. 

Shom

[James Robinson]

Hi, which genome?   Could you attach your igv.log file?  Its located in the "igv" folder in your home directory.

Also, could you try one of these development builds and see if it helps?  http://software.broadinstitute.org/software/igv/download_snapshot

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[Shom Goel]

Hi there

It is hg19. Log is attached.

I did download the Mac snapshot – I am not a computer person, unfortunately, and couldn’t find the IGV icon to open within the download package.

Many thanks for your help

Shom

 

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Shom Goel (B Med Sci, MBBS, FRACP, PhD)

Instructor in Medicine

Dana-Farber Cancer Institute

Boston MA

shom...@dfci.harvard.edu

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[James Robinson]

Hi Shom,

Thank you for your patience.   We have seen this problem within the Partners network sporadically but have not been able to reproduce it elsewhere.  

Could you try this as an experiment, shut down IGV and delete or rename the "genome" folder in the igv directory.   It is harmless to delete this,  it will be regenerated as needed.  

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/EE167D34-8C9D-475A-A985-30B9A249F259%40gmail.com.

[Shom Goel]

I see – thanks. I will try your suggestions and let you know fif I experience further problems,

I appreciate your help

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2Bptfzzf00ab1WKSkXcEw5Q3KV%3Da45FjBFC7X47-x2Mf6jw%40mail.gmail.com.

[James Robinson]

OK, please report back positive or negative results,  I would like to solve this problem.  

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/2EBD0238-4836-4F33-91A1-CA3D9D1C9E62%40gmail.com.

[James Robinson]

I just released version 2.4.19 which might work better in your network.   Please let me know.

There is a manual setup process to download and install the genome and fasta file locally which will permanently solve this issue if it persists with version 2.4.19.   

[Shom Goel]

Thank you James – I have downloaded 2.4.19 and will test it out on the network tomorrow.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2Bpu2zYHhSvrJnNDKvCPrAbHEjvx9KEsZqc8C6dODRB8zFw%40mail.gmail.com.