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segment fault when genotyping sv #131

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dodudoduding opened this issue Jul 7, 2023 · 0 comments
Open

segment fault when genotyping sv #131

dodudoduding opened this issue Jul 7, 2023 · 0 comments

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@dodudoduding
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Hello!

When I genotyped sv , I received warnings showing segment fault(core dumped), it's joint calling of only 2 samples (30X), and I also used avg_cov_by_readlen, max_files_open and threads but didn't work.

[2023-07-07 14:35:46.301] <info> SV genotyping region Chr1:1-10000
[2023-07-07 14:35:46.301] <info> Path to genome is '/media/data2/jiayi/20200524╓╪╫в╩═_Release/kan_chr.fa'
[2023-07-07 14:35:46.301] <info> Running with up to 10 threads.
[2023-07-07 14:35:46.301] <info> Copying data from 1 input SAM/BAM/CRAMs to local disk.
[2023-07-07 14:35:46.301] <info> Temporary folder is /tmp/graphtyper_230707_143546_Chr1_000000001.xCwgWW
[2023-07-07 14:35:46.301] <info> Genotype calling step starting.
[2023-07-07 14:35:46.302] <info> Padded region is: Chr1:1-211000
[2023-07-07 14:35:46.302] <info> Constructing graph.
[2023-07-07 14:35:46.410] <info> Calculating contig offsets.
Segmentation fault (core dumped)

Thank you!

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