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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.
The text was updated successfully, but these errors were encountered:
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: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 withodgi paths
command, and it lists the paths in the graph. I wonder if 500GB is still not enough memory? Any help would be appreciated.The text was updated successfully, but these errors were encountered: