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Seg fault when plotting a subgraph #603

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jikhashkya opened this issue Feb 13, 2025 · 0 comments
Open

Seg fault when plotting a subgraph #603

jikhashkya opened this issue Feb 13, 2025 · 0 comments

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@jikhashkya
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Hi,

I wanted to plot all the haplotype paths in a sub-graph but upon multiple tries it keeps failing with a segmentation fault. I ran the following command:
odgi viz -i subgraph_nodelist.run3.2.og -s '#' -o subgraph_nodelist.run3.2.png -X 1000 -P -t 32 and the program crashes with the following error:

[odgi::viz] Binned mode
[odgi::viz] bin width: 24372.8
[odgi::viz] image width: 1500
/var/spool/slurm/slurmd/job559751/slurm_script: line 8: 542721 Segmentation fault      (core dumped) odgi viz -i subgraph_nodelist.run3.2.og -s '#' -o subgraph_nodelist.run3.2.png -X 1000 -P -t 32

real    11m55.697s
user    4m27.446s
sys     2m29.272s

The program was run on a cluster with 500GB of RAM and 32 threads. The sub-graph consists of 10,903 nodes, 12,755 edges and a total length of 465,041 base pairs. I validated the graph with odgi validate command. I also checked to see if the graph has paths with odgi paths command, and it lists the paths in the graph. I wonder if 500GB is still not enough memory? Any help would be appreciated.

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