MSMC2 -I Range violation

[bxZhang996]

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Dear @stschiff I want to do population analysis using MSMC2, and I generate a combined input file with eight haplotypes like this (generate by 4 sample form 2 population) MayiVsCH_chr10.txt

and my command line was: ${MSMC}/msmc2 -t 15 -p 1*2+25*1+1*2+1*3 -o $OUTDIR/CH.msmc2 -I 0,1,2,3 $INDIR/MayiVsCH_chr*.txt ${MSMC}/msmc2 -t 15 -p 1*2+25*1+1*2+1*3 -o $OUTDIR/Mayi.msmc2 -I 4,5,6,7 $INDIR/MayiVsCH_chr*.txt

when I run this command, it reported an error. the log was, core.exception.RangeError@model/psmc_hmm.d(124): Range violation

??:? _d_arrayboundsp [0x5dcab1] ??:? void model.psmc_hmm.PSMC_hmm.runForward() [0x55b540] ??:? std.typecons.Tuple!(double[][], double[][2], double).Tuple expectation_step.singleChromosomeExpectation(in model.data.SegSite_t[], ulong, in model.propagation_core.PropagationCore) [0x590497] ??:? int expectation_step.getExpectation(in model.data.SegSite_t[][], model.psmc_model.PSMCmodel, ulong, ulong).__foreachbody5(ulong, ref const(model.data.SegSite_t[])) [0x5902af] ??:? void std.parallelism.ParallelForeach!(const(model.data.SegSite_t[])[]).ParallelForeach.opApply(scope int delegate(ulong, ref const(model.data.SegSite_t[]))).doIt() [0x5468ce] ??:? void std.parallelism.run!(void delegate()).run(void delegate()) [0x5ecbeb] ??:? void std.parallelism.Task!(std.parallelism.run, void delegate()).Task.impl(void*) [0x5ec6b7] ??:? void std.parallelism.AbstractTask.job() [0x61e67a] ??:? void std.parallelism.TaskPool.doJob(std.parallelism.AbstractTask*) [0x5eb10b] ??:? void std.parallelism.TaskPool.executeWorkLoop() [0x5eb281] ??:? void std.parallelism.TaskPool.startWorkLoop() [0x5eb227] ??:? void core.thread.context.Callable.opCall() [0x610060] ??:? thread_entryPoint [0x60fb43] ??:? [0x2af2975bae24] ??:? clone [0x2af2981eb34c]

Can you give me some help? Thank you, bx

[stschiff]

I will try and reproduce this, will be in touch.

[bxZhang996]

Thank you for your patient answer! I am so sorry to bother you. Last day, I found when I use the reference genome of Gullus.gullus(Galgal6), it can not call varient in chromosome 29, like this When I delete chr29.txt, it works. then, When I estimate population separation history, some result values(rCCR) are much higher than 1:

How can I solve this problem? Thank you, bx

[stschiff]

OK good. As for interpreting the rCCR: This can happen, perhaps due to bad phasing, or simply because of bad estimates of population sizes. The rCCR is simply the ratio of the cross-coalescence rate and the within-population coalescence rates. So perhaps you should look at all of them and see whether you understand where this comes from. There is no general advice here, I'm afraid

[bxZhang996]

thank you, I will check my dataset and try again

[camilamtza]

Hello @bxZhang996. I ran into the same problem. After several tries, MSMC2 was still indicating "Range violation" and I noticed I have some multihetsep files with no variants. Did you find a way around it? I'm working only with estimations of population size, if this changes something. Thank you.

[stschiff]

I don't understand. If you have empty multihetsep files, you need to obviously exclude them, because they provide no information. Or does that not solve the issue?