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labgem / PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes
https://ppanggolin.readthedocs.io
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Segmentation Fault at Partition #267

Open seajane opened 2 months ago

seajane commented 2 months ago

I was running through an analysis of 174 genbank files and have this error at the partitioning step:

zsh: segmentation fault ppanggolin partition -p pangenome.h5 --draw_ICL

/opt/homebrew/anaconda3/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 2 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

My version of ppanggolin is 2.1.0 and my laptop is Apple M3 Max with MacOS 14.6.1

jpjarnoux commented 2 months ago

Hi! I guess the problem comes from the processor and MacOS 14.6.1 (thank you for sharing these info, by the way). We did not test this version on our GitHub action. Why? Because Bioconda does not work correctly with Apple processors, and for a few months, GitHub has not used an Intel processor anymore but an Apple M processor for the recent MacOS version. So we are stuck to version MacOS 13 (see PR #220) Now, what I suggest is to do a manual installation to not use bioconda (be careful of the Python version). At the same time, could you share your genomes? That way, we could test it on Linux OS (Ubuntu, Fedora, etc.).
Unfortunately, I don't have a recent Mac available to test PPanGGOLiN, but I will try to find one if what I suggest does not work. Regards

seajane commented 2 months ago

I should have mentioned that I did have to install manually without conda and was unable to install the Aragorn dependency, but hoped it wouldn't matter. The genomes I used can be mostly downloaded from NCBI with the exception of some proprietary sequences. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2701