Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Blocker
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Resolution: Done
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Labels:
Description
Hi, since updating to IGB 8.5.2, I get frequent crashes. I am running it on a Retina iMac under OS X 10.10.5, with 32 GB of RAM. The crashes appear to happen when I attempt to load a track, or resize the window, but only intermittently, so I can't really nail down what's causing it - just that its happens multiple times per hour as I'm working with it. Didn't happen with the previous version. Let me know if there is anything I can check on my end. I will try to reinstall the older version until this is figured out.
On another topic, the ability to export tracks as .sgr files disappeared a few versions ago - I often found this extremely useful. Some of our data files are binary graph (.bar), and this was a quick and easy way for us to convert them to text graph (.sgr) files for use in some of our R programs. The .gr files don't have the chromosome arm column, which we need. If there is a way to bring back the .sgr export it would be great!
Thanks,
Dale Dorsett
Reporter: Dale Dorsett
E-mail: dorsettd@slu.edu
Attachments
Activity
To: Dale Dorsett <dorsettd@slu.edu>
From: David Norris <dcnorris@uncc.edu>
CC: Ann Loraine, Mason Meyer, John Eckstein
Date: Jan 26, 2016 2:09:49 PM
Subject: Follow up
Hi Dale,
First, let me apologize for the delayed response to your report. We had an issue with our server failing to send email notifications that has now been resolved.
I have not heard any similar reports about the crashing issue you have reported. Could you look in your IGB application directory for the existence of any hs_err_pid*.log log files? They should be located in /Applications/Integrated\ Genome\ Browser/ on Mac OSX if they exist.
If you could send me a crash report I would very much appreciate it.
I have created a feature request for restoring the sgr export feature. I do not recall if there was a good reason we removed this feature, or if this is an unintentional regression, but I will follow up on this to see if it is feasible to restore it in the next minor release (~sometime in next few weeks).
Best Regards,
David Norris
To: David Norris <dcnorris@uncc.edu>
From: Dale Dorsett <dorsettd@slu.edu>
CC: Ann Loraine, Mason Meyer, John Eckstein
Date: Feb 9, 2016 2:23:59 PM
Subject: Follow up
Hi David,
No worries - I downgraded to 8.4.4 and things have been working smoothly. I found one hs_err_pid*.log, which is attached. Hopefully its the one that recorded the crashes I was getting with the 8.5 versions - its the only one I found.
I realized later that the current bedgraph file export from IGB is on nt basis with identical start and stop positions so it was easy to write a script or use a unix cut command to remove one column and convert it to an sgr file, so that works ok if it turns out that it is a problem putting back the sgr export - only adds one quick step to the workflow!
Thanks,
-Dale