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kcleal / gw

Genome browser and variant annotation
MIT License
282 stars 7 forks source link

segfault after typing `help` #42

Closed jamestwebber closed 3 months ago

jamestwebber commented 3 months ago

Describe the bug I was excited to try this out! But immediately hit a segfault after I loaded some BAM files and typed /help. 😢

To Reproduce Steps to reproduce the behavior:

I installed with conda create -n gw -c bioconda gw, ran gw hg38 to start a session, dragged four BAMs into the window, and the typed /help to see the commands available.

System (please complete the following information):

BioFalcon commented 3 months ago

I am also experiencing this same issue, same kind of setup (macOS Sonoma on an Intel Processor), also for some weird reason when running GW it shows version v0.1.0 instead v1.0.0, probably a typo?

kcleal commented 3 months ago

Hi @jamestwebber, That's not good! It may be an issue with conda binary. Would you be able to install use the desktop app or brew instead of conda? There seems to be a few issues with the conda install at the moment. I will see if I can reproduce the error my end...

Also, does it work if you drag and drop a single bam, then navigate to a region?

jamestwebber commented 3 months ago

Unfortunately the installer doesn't work either because OS X won't let me open it (and our IT rules are too strict for me to override this).

Screenshot 2024-07-29 at 12 27 52
jamestwebber commented 3 months ago

Also, does it work if you drag and drop a single bam, then navigate to a region?

Also segfaults :/

kcleal commented 3 months ago

Ok, are you able to install with brew? My apologies, I will look in to this ASAP

kcleal commented 3 months ago

Hi @BioFalcon, Where do you see the v0.1.0?

jamestwebber commented 3 months ago

I see it in the download link in the console:

â–€ https://github.com/kcleal/ref_genomes/releases/download/v0.1.0

Also, the brew installation segfaulted as well. I'll check back later!

kcleal commented 3 months ago

Thanks for trying. The ref genomes v0.1.0 is related to the GitHub repo for the reference genomes, so is nothing to worry about.

I'm afraid I don't know why you have a segfault. If you could run the following test, it would be helpful for me:

gw hg38 -r chr1 -n > /dev/null

Also, if you have a local reference genome handy, would you be able to replace hg38 with the path to your reference genome? I'm wondering if the online reference genome is causing an issue

BioFalcon commented 3 months ago

I tried substituting to a local genome, still het the segmentation fault:

zsh: segmentation fault gw -b RepMasker.bed ce11.fa

kcleal commented 3 months ago

Ok thanks for trying. Are you also using intel macOS Sonoma @BioFalcon? I will have some time tomorrow to try and fix this.

BioFalcon commented 3 months ago

Yes, Intel Mac with Sonoma

On Tue, 30 Jul 2024, 16:25 Kez Cleal, @.***> wrote:

Ok thanks for trying. Are you also using intel macOS Sonoma @BioFalcon https://github.com/BioFalcon? I will have some time tomorrow to try and fix this.

— Reply to this email directly, view it on GitHub https://github.com/kcleal/gw/issues/42#issuecomment-2258486242, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEICXCYQL3EX4FNG4AF3G3LZO6O4DAVCNFSM6AAAAABLUOL7ECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJYGQ4DMMRUGI . You are receiving this because you were mentioned.Message ID: @.***>

kcleal commented 3 months ago

I managed to repeat this issue on an intel Mac where GW crashed if you type in a region ID or load a bam after start up. I have hopefully now fixed the issue in v1.0.1. I will need someone else to confirm if the issue is resolved. I was able to install a working version using conda on my macOS intel test machine.

jamestwebber commented 3 months ago

It works! 🎉 Checking it out now, thanks for the fix.