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squid errors #18

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jchenpku opened this issue Oct 7, 2019 · 1 comment
Open

squid errors #18

jchenpku opened this issue Oct 7, 2019 · 1 comment

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@jchenpku
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jchenpku commented Oct 7, 2019

[Mon Oct 7 13:51:39 2019] Start reading bam file.
[Mon Oct 7 13:51:58 2019] Finish sorting Chimeric bam reads.
[Mon Oct 7 13:52:00 2019] Finish removing PCR duplicates.
[Mon Oct 7 13:52:01 2019] Building nodes. |bamdiscordant|=502321
[Mon Oct 7 14:17:55 2019] Building nodes, finish seeding.
squid: src/SegmentGraph.cpp:664: void SegmentGraph_t::BuildNode_STAR(const std::vector&, SBamrecord_t&, std::string): Assertion `(vNodes[i].Chr!=vNodes[i+1].Chr) || (vNodes[i].Chr==vNodes[i+1].Chr && vNodes[i].Position+vNodes[i].Length<=vNodes[i+1].Position)' failed.
Aborted (core dumped)

@Congm12
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Congm12 commented Oct 8, 2019

Could you provide more information about in what dataset you have this error and the command you used to process it?

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