vgteam
Receiving "warning:[XG] Loading an out-of-date XG format" with newest version of vg
I recently installed the newest vg version a few days ago from the vg git page on a machine I'm running the tubemaps sever on. Every time I boot it up, I get:
warning:[XG] Loading an out-of-date XG format. In-memory conversion between versions can be time-consuming. For better performance over repeated loads, consider recreating this XG with 'vg index' or upgrading it with 'vg xg'. ERROR: Signal 11 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_vYyJy5/stacktrace.txt
At the top, right when it loads, with the sample "BRCA" data (or with my own data). Furthermore, none of my own personal XG files I created with the "prepare_vg" script, and mounted in the correct folder, want to load for similar reasons.
As of today we made a major breaking change with the xg format. I suggest rebuilding the indexes. I'm sorry for the trouble this might cause. I don't expect there will be future breaking changes of this nature.
On Tue, Sep 10, 2019, 19:26 Brian Nadon [email protected] wrote:
I recently installed the newest vg version a few days ago from the vg git page on a machine I'm running the tubemaps sever on. Every time I boot it up, I get:
warning:[XG] Loading an out-of-date XG format. In-memory conversion between versions can be time-consuming. For better performance over repeated loads, consider recreating this XG with 'vg index' or upgrading it with 'vg xg'. ERROR: Signal 11 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_vYyJy5/stacktrace.txt
At the top, right when it loads, with the sample "BRCA" data (or with my own data). Furthermore, none of my own personal XG files I created with the "prepare_vg" script, and mounted in the correct folder, want to load for similar reasons.
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That's good to know. However, I was getting this issue as far back as last week too, and I pulled the latest version of vg around then too. Do I need to do a clean install of both tubemaps and vg, or what should I do?
Sorry, I think I've got my wires crossed and thought I was responding to a message in the vg issues (not tubemap). I can't say I understand what's causing this, and I'm not sure what vg version is in the docker image for this project.
On Tue, Sep 10, 2019 at 10:26 PM Brian Nadon [email protected] wrote:
That's good to know. However, I was getting this issue as far back as last week too, and I pulled the latest version of vg around then too. Do I need to do a clean install of both tubemaps and vg, or what should I do?
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