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I was mapping a subset of nanopore reads to a subset of a gfa, and everything worked fine under my previous minigraph version (0.15-r426) but then repeatedly failed an assertion in the latest version (0.15-r434-dirty) from the same command minigraph -t 2 -xlr --vc unitigs.gfa nanopore.fq.gz
Thank you! Is it possible to share me with your data? I don't see the crash on my data. I had a look at code and recent changes but it is not immediately clear to me what could go wrong. When running minigraph, you may use
make asan=1
minigraph --dbg-kalloc --dbg-qname -t1
asan=1 and --dbg-kalloc helps to expose memory bugs. --dbg-qname prints query name. -t1 uses one thread. With these settings, you may be able to catch the read that breaks minigraph.
BTW, the current github HEAD has features backported from minimap2-2.24.
I was mapping a subset of nanopore reads to a subset of a gfa, and everything worked fine under my previous minigraph version (0.15-r426) but then repeatedly failed an assertion in the latest version (0.15-r434-dirty) from the same command
minigraph -t 2 -xlr --vc unitigs.gfa nanopore.fq.gz
error was
Same code segfaults at 011f4a2, and crashes at 94289c8 with the following
So the assertion error seems to appear at 0c9086b.
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