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A Segmentation fault occurred in the sambamba markdup #520

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Xiangyue-Meng opened this issue Aug 20, 2024 · 0 comments
Open

A Segmentation fault occurred in the sambamba markdup #520

Xiangyue-Meng opened this issue Aug 20, 2024 · 0 comments
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@Xiangyue-Meng
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When using sambamba to remove PCR duplicates, the code I use is:
sambamba markdup --overflow-list-size 600000 --tmpdir='./' -r C2C12-50cell-1.bam C2C12-50cell-1.rmdup.bam
Segmentation faults(core dumped) occur when duplicates are removed after they are identified.
Because I had run different data before, I could run it out, so I thought if the version was too low, I updated sambamba.
The above error no longer occurs after the update, but sambamba stops at identifying duplicates because the cpu usage is 0.

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