Software hang when dealing with large custom SNP-databases

FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.

GNU General Public License v3.0

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Software hang when dealing with large custom SNP-databases #41

Open jaclew opened 9 months ago

jaclew commented 9 months ago

I made a database with many (>2000 SNPs for a reference) added custom SNPs which lead to the software hanging during SNP calling. I identified the hang to be due to suboptimal usage of multiprocessing Queues and believe that the Queue was filled, leading to a stalled execution. Please consider the pull request.

Pull request: https://github.com/FOI-Bioinformatics/CanSNPer2/pull/40