Closed JosephLalli closed 1 year ago
I'm trying to get shapeit5 to export graphs for subsequent determination of recombination sites in trios using duohmm. However, I get the following error:
[SHAPEIT5] phase_common (jointly phase multiple common markers) * Author : Olivier DELANEAU, University of Lausanne * Contact : olivier.delaneau@gmail.com * Version : 5.1.1 / commit = 990ed0d / release = 2023-05-08 * Run date : 04/06/2023 - 16:32:08 Files: * Input : [input.bcf.gz] * Genetic Map : [PAR2.gmap.gz] * Output : [output.graph] * Output format : [graph] Parameters: * Seed : 15052011 * Threads : 64 threads * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] * PBWT : [window = 5cM / depth = 8 / modulo = 0.1 / mac = 5 / missing = 0.1] * HMM : [window = 5cM / Ne = 15000 / Recombination rates given by genetic map] * FILTERS : [snp only = 0 / MAF = 0.001] Reading genotype data: * VCF/BCF scanning done (0.02s) + Variants [#sites=3018 / region=chrX:153925834-154259566] - 5290 sites removed in main panel [below MAF threshold] + Samples [#target=3202 / #reference=0] * VCF/BCF parsing done (0.09s) + Genotypes [0/0=86.805%, 0/1=8.267%, 1/1=4.854%, ./.=0.075%, 0|1=0.000%] Setting up genetic map: * GMAP parsing [n=179] (0.02s) * cM interpolation [s=178 / i=2840] (0.00s) * Region length [319083 bp / 0.4 cM] * HMM parameters [Ne=15000 / Error=0.0001 / #rare=0] .... Finalization: * HAP solving (0.04s) * HAP update (0.02s) * H2V transpose (0.01s) terminate called after throwing an instance of 'boost::wrapexcept<boost::bad_any_cast>' what(): boost::bad_any_cast: failed conversion using boost::any_cast Aborted (core dumped)
I am using the PAR2 region as a short test region, but the error applies to any chromosomal region I test. Can this bug be fixed?
Sorry about this. Please keep using S4 for this as I have not yet ported/tested this code into S5.
I'm trying to get shapeit5 to export graphs for subsequent determination of recombination sites in trios using duohmm. However, I get the following error:
I am using the PAR2 region as a short test region, but the error applies to any chromosomal region I test. Can this bug be fixed?