Error when using tree sequence recording in conditional simulations

[olivia-johnson]

Hi everyone,

Following the new update, I have found that my conditional simulation that includes tree sequence recording returns an error when it restarts if the condition could not be met. The error is "(Species::InstantiateSLiMObjectsFromTables): (internal error) remembered_genomes is not empty" and it invalidates the simulation. I think I need to clear the individuals from the memory when the simulation restarts, but I'm not sure how to do that.

I have adapted recipe 9.2 such that it returns the same error (see minimal example below).

Thanks so much for your help!
Olivia

// Minimal example: Conditional simulation with tree sequence recording



initialize() {

   initializeMutationRate(0);

   initializeMutationType("m1", 0.0, "f", 0.0);// introduced mutation

   initializeGenomicElementType("g1", m1, 1.0);

   initializeGenomicElement(g1, 0, 99999);

   initializeRecombinationRate(1e-8);

   initializeTreeSeq();

}

1 early() {

   // save this run's identifier, used to save and restore

   defineConstant("simID", getSeed());

   sim.addSubpop("p1", 500);

}

1000 late() {

   // save the state of the simulation

   sim.treeSeqOutput(tempdir() + "slim_" + simID + ".trees");

   // introduce the sweep mutation

   target = sample(p1.genomes, 1);

   target.addNewDrawnMutation(m1, 10000);

}

1000:100000 late() {

   rInd= sample(p1.individuals, 10);

   sim.treeSeqRememberIndividuals(rInd);

   if (sim.countOfMutationsOfType(m1) == 0)

   {
       fixed = (sum(sim.substitutions.mutationType == m1) == 1);

       if (fixed){

           cat(simID + ": FIXED\n");

           sim.simulationFinished();
       }

       else

       {
           cat(simID + ": LOST at " +sim.cycle+" - RESTARTING\n");

           // go back to tick 1000

           sim.readFromPopulationFile(tempdir() + "slim_" + simID + ".trees");

           // start a newly seeded run

           setSeed(rdunif(1, 0, asInteger(2^62) - 1));

           // re-introduce the sweep mutation

           target = sample(p1.genomes, 1);

           target.addNewDrawnMutation(m1, 10000);
       }

   }

}

[bhaller]

Hi @olivia-johnson. Thanks very much for the bug report. I'll look into it as soon as I can, perhaps later today. I think it will be an easy fix; it's just a case that we haven't tested, and so it slipped through the cracks. (@petrelharp perhaps it would be good for you and I to both add a test that hits this case, in our respective testing suites!)