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heche-psb / wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
https://wgdv2.readthedocs.io/en/latest/
GNU General Public License v3.0
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Segmentation fault (core dumped) #16

Closed ZhaoHang-bio closed 7 months ago

ZhaoHang-bio commented 7 months ago

Hi,

I am currently testing the wgd v2 software with the following command:

wgd dmd sample.longestcds.fa -o 01.step-dmd -n 10 However, I encountered an error message:

12:31:22 INFO     This is wgd v2.0.23                                                                                         cli.py:32     
Segmentation fault (core dumped)

Could you please advise on how to resolve this issue?

heche-psb commented 7 months ago

Hi, it seems to be a memory issue. Can you increase the memory to 5G or 10G and try again?

ZhaoHang-bio commented 7 months ago

I attempted to run test data using the wgd v2.0.23 software on a compute node with 6T of memory.

wgd dmd egu1000.fasta

However, the process still ended unexpectedly with a same error :

11:35:23 INFO     This is wgd v2.0.23 cli.py:32 
Segmentation fault (core dumped)
heche-psb commented 7 months ago

The "Segmentation fault (core dumped)" is showing that the program has problems accessing the memory. Do you "qsub" the job with enough memory required or just run the command locally on the cluster/HPC? The latter will be restricted on certain HPC.