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aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.
GNU General Public License v3.0
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contig failing on bubble pinching #7

Closed travc closed 9 years ago

travc commented 9 years ago

It segfaults very shortly after Start to pinch bubbles.

I had seen the error message Error : Number of vertex is out of range, but can't seem to get it to reproduce that at the moment.

I'm running from a fresh pull (2015-09-28) and build on Ubuntu 14.04.3 LTS.

travc commented 9 years ago

Ok... This may have been due to some issue when compiling. I have no clue how. When I rebuilt with debug=1 and -j20, it ended up failing to resolve some symbols which should have clearly been there. However, when I built with just a single thread (no -j20') it linked fine and didn't hit the above bug.

Anyways, maybe there is something with the way you have your Makefiles structured that leads to odd results when making with multiple jobs.

For what it's worth, I using: GNU Make 3.81 gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4

I'm going to close this, but you might want to look into it. Sorry, I don't have the time.

aquaskyline commented 9 years ago

This looks like a compiler optimization problem. When debug is on, the compiler optimization option switches to level 0, thus bypassing the problem.