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karel-brinda / NanoSim-H

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
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training stuck in model fitting #21

Open thackl opened 3 years ago

thackl commented 3 years ago

Hi, I have some lambda spike-in data from a recent run and wanted to use it to train a model for that run. But when I ran

nanosim-h-train -i lambda.fa lambda.fna np-prof-lambda

it just kept Running 'R CMD BATCH '--args prefix="np-prof-lambda"' "/home/thackl/.local/lib/python3.8/site-packages/nanosimh/model_fitting.R"' forever.

It's just 2MB of reads, so I'm guessing it should be quick. But maybe it's not enough data for training?

In any case, here are the data I used, in case you need it: lambda.fna lambda.fa

molleraj commented 3 years ago

Hey there, I am getting the same problem, but with amplicons from S. aureus genomes. I am trying it in a new directory to see if leftover intermediary files were the problem.

karel-brinda commented 3 years ago

Thanks for the report! Unfortunately, I'm not currently able to work on this, but I'm happy to consider a pull request.