Creating .Genome hung and stuck on IGV_2.3.89

[Alex Chitsazan]

I'm having trouble creating a .genome. I'm doing this in dogs, in which I'm trying to version control our GTF for CanFam3.1.  

If I load my appropriate files of:

 1. fasta (`Canis_familiaris.CanFam3.1.dna_rm.toplevel.fa`) found at ftp://ftp.ensembl.org/pub/release-85/fasta/canis_familiaris/dna/

2. GTF ('Canis_familiaris.CanFam3.1.85.gtf.gz') found at ftp://ftp.ensembl.org/pub/release-85/gtf/canis_familiaris

It hangs on "loading genome" and when it eventually loads after ~5 min, the gene track doesn't show up. Even more weird, if I load the .genome created from igv_2.3.89 (which had the problem previously stated) in the web igv_2.3, it loads fine. Any idea as to why this could be?

- Alex

[James Robinson]

The log shows you ran out of memory,  probably because of the size of the gtf file.   Which download option did you use for the 2.3.89 version?  

BTW,  the web page also launches 2.3.89, which you can verify with "Help > About".    Which of the webpage links did you click (there are 4).

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[Alex Chitsazan]

Wierd. Memory on my computer? I dowloaded from the main link posted on the homepage titled "Downloads" that states "Download the IGV desktop application and igvtools"

Alex

On Friday, January 6, 2017 at 3:54:14 PM UTC-8, Jim Robinson wrote:

The log shows you ran out of memory,  probably because of the size of the gtf file.   Which download option did you use for the 2.3.89 version?  

BTW,  the web page also launches 2.3.89, which you can verify with "Help > About".    Which of the webpage links did you click (there are 4).

On Fri, Jan 6, 2017 at 2:49 PM, Alex Chitsazan <chitsa...@gmail.com> wrote:

I'm having trouble creating a .genome. I'm doing this in dogs, in which I'm trying to version control our GTF for CanFam3.1.  

If I load my appropriate files of:

 1. fasta (`Canis_familiaris.CanFam3.1.dna_rm.toplevel.fa`) found at ftp://ftp.ensembl.org/pub/release-85/fasta/canis_familiaris/dna/

2. GTF ('Canis_familiaris.CanFam3.1.85.gtf.gz') found at ftp://ftp.ensembl.org/pub/release-85/gtf/canis_familiaris

It hangs on "loading genome" and when it eventually loads after ~5 min, the gene track doesn't show up. Even more weird, if I load the .genome created from igv_2.3.89 (which had the problem previously stated) in the web igv_2.3, it loads fine. Any idea as to why this could be?

- Alex

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[James Robinson]

Yes, that link takes you to a page with many download and web launch options.   Which exactly did you use?

[James Robinson]

BTW that assembly is available via "Load genome from server".   Its  listed as  "Dog (canFam3)".   The annotation set is different but sequence is the same,  you can load the gtf separately as a track.

[Alex Chitsazan]

Oh great I did not realize you could load the gtf as a track. Maybe that is how I should do it. The "mac app" download of 2.3.89

Thanks!

Alex