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dfguan / purge_dups

haplotypic duplication identification tool
MIT License
205 stars 20 forks source link

Segmentation fault #152

Open jeramiahsmith opened 2 weeks ago

jeramiahsmith commented 2 weeks ago

I have used purge_dups on various assemblies recently but have run into an issue where purge_dups dies partway through processing split.self.paf.gz with a segfault while using 4GB of ram. I have replicated this on several machines with up to 1TB ram available. Would love to know if there is a solution to this.

jeramiahsmith commented 2 weeks ago

happy to share the .paf file ~2Gb gzipped if it is helpful in assessing this issue.

malvaradol commented 1 week ago

I'm currently having the same issue, and I spotted that minimap2 did not run properly. I'm rerunning minimap2, maybe check for any corrupted files from the first stepts. I will let you know if this solved the problem.