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Segfault when running on AllTheBacteria dataset #48

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sebschmi opened this issue Jan 13, 2025 · 0 comments
Open

Segfault when running on AllTheBacteria dataset #48

sebschmi opened this issue Jan 13, 2025 · 0 comments

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@sebschmi
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sebschmi commented Jan 13, 2025

Input:

AllTheBacteria dataset downloaded from https://osf.io/xv7q9/.

Command:

cuttlefish build -m 128 -s references.fa -k 27 -t 128 -o unitigs -w workdir --ref -c 1

The dataset is about 9.2TB large and the server has about 21TB total disk space.
Alternatively running with -k 63 seems to get further, but so far it hasn't terminated yet, so I can't say if it works.

Log:

Constructing the compacted reference de Bruijn graph for k = 27.

Enumerating the edges of the de Bruijn graph.
***************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
Stage 1: 100%
Warning: using counter_max == 1 will cause not storying counters in KMC output file, all counters will be assumed to be 1. This is experimental and is not currently supported in kmc_tools. Will be implemented soon.
Stage 2: 93%
*Command terminated by signal 11
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