GW window all black

Question

GW window all black

p-levy opened this issue 2 years ago · 11 comments

Hi, thanks for developing this great tool!
I'm having an issue when trying to run gw. The simple command gw GRCh38.primary_assembly.genome.fa opens a GW window that stays all black. I also tried loading a bam file but it didn't help.
I installed gw via conda in a new environment. I'm working on Mac OS.
Any idea what could be the problem? I don't get any error message.

kcleal commented 2 years ago

Great!

Answer 1 · 2022-11-17T10:45:21.000Z

Possibly you just need to specify a region. Try adding one with :goto chr1:1-20000 as a command (make sure to click on the gw window first), or from the command line -r chr1:1-20000

Answer 2 · 2022-11-17T10:57:11.000Z

Sorry I forgot to mention that I also tried that and it doesn't help.

For some reason when I try now specifying the region it returns a Segmentation fault: 11.

Answer 3 · 2022-11-17T11:00:34.000Z

Does it work if you specify a bam file on the command line?

gw GRCh38 -r chr1:1-20000 -b your.bam

Im actually in the process of fixing a few bugs related to opening regions without a bam file, so I might have already addressed this. I will try and commit the changes within the hour. I think some of these bugs were introduced in 0.2.0, so you can try one of the older versions if you wish.

Answer 4 · 2022-11-17T11:06:20.000Z

Unfortunately it looks the same when I specify a bam file from the command line.

I'll try some older versions!

Answer 5 · 2022-11-17T11:14:45.000Z

I downgraded to version 0.1.7 and it looks the same

Answer 6 · 2022-11-17T11:17:55.000Z

Ok, that is a bit confusing. Would you mind sending me a small sample of that bam file clealk@cardiff.ac.uk? You can use samtools view -bh your.bam chr1:1-20000 > test.bam. Im not sure of the problem at the moment, sorry.

Answer 7 · 2022-11-17T11:32:36.000Z

Thanks for the bam file. Weirdly, I have no problems viewing it. It could be something to do with your graphics drivers - what system are you using? If you are using an old Mac this might cause some problems. Also you might be better off trying to build gw from source, although you will need to install glfw and htslib beforehand

Answer 8 · 2022-11-17T11:38:05.000Z

A little old, but still working pretty good for most applications!

I'll try building from source. Thanks!

Answer 9 · 2022-11-17T11:42:05.000Z

I have tested gw on a 2014 mac so it should work on yours. Hopefully building from source will do it - let me know

Answer 10 · 2022-11-17T12:11:37.000Z

It worked after building from source! :)