1425 smcpp.commands.command DEBUG ['/usr/local/bin/smc++', 'split', '--cores', '52', '-v', '-o', '/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts', '/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/Wild_Knots.final.json', '/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/smcPP_Estimate_Landrace_knots.final.json', 'Wild_Landrace_Ann1238_AllReads_Chr01.smc.gz', 'Wild_Landrace_ANN1198_Chr01.smc.gz', 'Wild_Landrace_IA2W-11_Chr01.smc.gz', 'Wild_Landrace_Ann1238_AllReads_Chr13.smc.gz', 'Wild_Landrace_ANN1198_Chr13.smc.gz', 'Wild_Landrace_IA2W-11_Chr13.smc.gz', 'Wild_Landrace_Ann1238_AllReads_Chr15.smc.gz', 'Wild_Landrace_ANN1198_Chr15.smc.gz', 'Wild_Landrace_IA2W-11_Chr15.smc.gz', 'Wild_Landrace_MO1W-33_Chr15.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr15.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr15.smc.gz', 'Wild_Landrace_MO1W-33_Chr13.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr13.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr13.smc.gz', 'Wild_Landrace_MO1W-33_Chr14.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr14.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr14.smc.gz', 'Wild_Landrace_MO1W-33_Chr01.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr01.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr01.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr01.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr01.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr01.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr13.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr13.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr13.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr14.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr14.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr14.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr15.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr15.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr15.smc.gz', 'Landrace_Wild_Arikara_Chr13.smc.gz', 'Landrace_Wild_Hidatsa_Chr13.smc.gz', 'Landrace_Wild_Mandan1_PPN046_Chr13.smc.gz', 'Landrace_Wild_Havasupai_Chr13.smc.gz', 'Landrace_Wild_Laguna_Pueblo_Chr13.smc.gz', 'Landrace_Wild_Hopi_real_NEW_Chr13.smc.gz']
1425 smcpp.commands.command DEBUG Namespace(Nmax=1000.0, Nmin=0.001, algorithm='L-BFGS-B', base='model', command='split', cores=52, data=['Wild_Landrace_Ann1238_AllReads_Chr01.smc.gz', 'Wild_Landrace_ANN1198_Chr01.smc.gz', 'Wild_Landrace_IA2W-11_Chr01.smc.gz', 'Wild_Landrace_Ann1238_AllReads_Chr13.smc.gz', 'Wild_Landrace_ANN1198_Chr13.smc.gz', 'Wild_Landrace_IA2W-11_Chr13.smc.gz', 'Wild_Landrace_Ann1238_AllReads_Chr15.smc.gz', 'Wild_Landrace_ANN1198_Chr15.smc.gz', 'Wild_Landrace_IA2W-11_Chr15.smc.gz', 'Wild_Landrace_MO1W-33_Chr15.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr15.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr15.smc.gz', 'Wild_Landrace_MO1W-33_Chr13.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr13.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr13.smc.gz', 'Wild_Landrace_MO1W-33_Chr14.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr14.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr14.smc.gz', 'Wild_Landrace_MO1W-33_Chr01.smc.gz', 'Wild_Landrace_ann01_cwIA_Chr01.smc.gz', 'Wild_Landrace_ann04_nwAR_Chr01.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr01.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr01.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr01.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr13.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr13.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr13.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr14.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr14.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr14.smc.gz', 'Wild_Landrace_ann39_ncNE_Chr15.smc.gz', 'Wild_Landrace_ann34_cwKS_Chr15.smc.gz', 'Wild_Landrace_ann10_ccIL_Chr15.smc.gz', 'Landrace_Wild_Arikara_Chr13.smc.gz', 'Landrace_Wild_Hidatsa_Chr13.smc.gz', 'Landrace_Wild_Mandan1_PPN046_Chr13.smc.gz', 'Landrace_Wild_Havasupai_Chr13.smc.gz', 'Landrace_Wild_Laguna_Pueblo_Chr13.smc.gz', 'Landrace_Wild_Hopi_real_NEW_Chr13.smc.gz'], em_iterations=20, ftol=0.0001, lambda_=None, length_cutoff=None, multi=False, no_initialize=False, nonseg_cutoff=None, outdir='/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts', polarization_error=0.5, pop1='/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/Wild_Knots.final.json', pop2='/global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/smcPP_Estimate_Landrace_knots.final.json', regularization_penalty=6, seed=0, thinning=None, timepoints=None, unfold=False, verbose=1, w=100, xtol=0.1)
1426 smcpp.analysis.base INFO theta: 0.000100
1427 smcpp.analysis.base INFO rho: 0.000100
1427 smcpp.analysis.base DEBUG Polarization error p=0.500000
1427 smcpp.data_filter DEBUG LoadData()
1427 smcpp.data_filter INFO Loading data...
120053 smcpp.data_filter INFO 6.94 Gb of data
120054 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Mandan1_PPN046_Chr13.smc.gz')
120056 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Havasupai_Chr13.smc.gz')
120056 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,   0,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,   0,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann01_cwIA_Chr14.smc.gz')
120057 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann39_ncNE_Chr01.smc.gz')
120057 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann01_cwIA_Chr15.smc.gz')
120058 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_MO1W-33_Chr15.smc.gz')
120058 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann04_nwAR_Chr13.smc.gz')
120058 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann34_cwKS_Chr13.smc.gz')
120059 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,  -1,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,  -1,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann34_cwKS_Chr14.smc.gz')
120059 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Hidatsa_Chr13.smc.gz')
120059 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann39_ncNE_Chr15.smc.gz')
120060 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1,  0,  0, ...,  0,  0, 14],
       [ 1,  0,  0, ...,  0,  0, 16],
       [ 1,  0,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_Ann1238_AllReads_Chr01.smc.gz')
120060 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_Ann1238_AllReads_Chr15.smc.gz')
120060 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Arikara_Chr13.smc.gz')
120061 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,  -1,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,  -1,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann04_nwAR_Chr14.smc.gz')
120061 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ANN1198_Chr15.smc.gz')
120062 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,  -1,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,  -1,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann39_ncNE_Chr14.smc.gz')
120062 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann04_nwAR_Chr01.smc.gz')
120062 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann10_ccIL_Chr15.smc.gz')
120063 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,  -1,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,  -1,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_MO1W-33_Chr14.smc.gz')
120063 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_IA2W-11_Chr13.smc.gz')
120063 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann34_cwKS_Chr01.smc.gz')
120064 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann39_ncNE_Chr13.smc.gz')
120064 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann34_cwKS_Chr15.smc.gz')
120064 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_MO1W-33_Chr01.smc.gz')
120065 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ANN1198_Chr01.smc.gz')
120065 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann10_ccIL_Chr13.smc.gz')
120066 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Laguna_Pueblo_Chr13.smc.gz')
120066 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann04_nwAR_Chr15.smc.gz')
120066 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 86,  -1,   0, ...,   0,   0,   0],
       [350,  -1,   0, ...,   0,   0,   0],
       [ 89,  -1,   0, ...,   0,   0,   0],
       ...,
       [  7,  -1,   0, ...,   0,   0,   2],
       [ 16,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann10_ccIL_Chr14.smc.gz')
120067 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 45,  -1,   0, ...,   0,   0,   0],
       [  6,  -1,   0, ...,   0,   0,   2],
       [  6,  -1,   0, ...,   0,   0,   2],
       ...,
       [ 28,  -1,   0, ...,   0,   0,   0],
       [122,  -1,   0, ...,   0,   0,   0],
       [  1,   0,   0, ...,   0,   0,  54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_IA2W-11_Chr15.smc.gz')
120067 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ANN1198_Chr13.smc.gz')
120067 smcpp.data_filter DEBUG Contig(pid=('LRE', 'Wild'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    2],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    0],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,  294]], dtype=int32), n=array([ 52, 294]), a=array([2, 0]), fn='Landrace_Wild_Hopi_real_NEW_Chr13.smc.gz')
120068 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_MO1W-33_Chr13.smc.gz')
120068 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,   -1,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann01_cwIA_Chr13.smc.gz')
120068 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[2476,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,    0],
       [   4,   -1,    0, ...,    0,    0,    0],
       ...,
       [   6,   -1,    0, ...,    0,    0,    2],
       [ 493,   -1,    0, ...,    0,    0,    0],
       [   1,    0,    0, ...,    0,    0,   54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_Ann1238_AllReads_Chr13.smc.gz')
120069 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann10_ccIL_Chr01.smc.gz')
120069 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_IA2W-11_Chr01.smc.gz')
120070 smcpp.data_filter DEBUG Contig(pid=('Wild', 'LRE'), data=array([[ 1, -1,  0, ...,  0,  0, 14],
       [ 1, -1,  0, ...,  0,  0, 16],
       [ 1, -1,  0, ...,  0,  0, 18],
       ...,
       [ 5, -1,  0, ...,  0,  0,  2],
       [42, -1,  0, ...,  0,  0,  0],
       [ 1,  0,  0, ...,  0,  0, 54]], dtype=int32), n=array([292,  54]), a=array([2, 0]), fn='Wild_Landrace_ann01_cwIA_Chr01.smc.gz')
120070 smcpp.data_filter INFO 2 populations
120070 smcpp.data_filter DEBUG RecodeNonseg(cutoff=None)
214544 smcpp.data_filter DEBUG Compress()
363224 smcpp.data_filter DEBUG BreakLongSpans(cutoff=100000)
364776 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
367400 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
371926 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
378446 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
384155 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
389019 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
392723 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
395317 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
399837 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
404288 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
408076 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
413924 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
419796 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
423583 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
428118 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
433739 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
439379 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
445881 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
451594 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
457235 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
461631 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
466279 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
470822 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
474565 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
480361 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
486953 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
491545 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
494130 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
497916 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
503543 smcpp.estimation_tools DEBUG Long missing spans:
[32265297] (base pairs)
509160 smcpp.estimation_tools DEBUG Long missing spans:
[68296528] (base pairs)
512890 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
515476 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
518087 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
520668 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
523289 smcpp.estimation_tools DEBUG Long missing spans:
[94778214 17700007] (base pairs)
527972 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
534601 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
541201 smcpp.estimation_tools DEBUG Long missing spans:
[3189915] (base pairs)
544632 smcpp.data_filter DEBUG DropSmallContigs(cutoff=100000)
551972 smcpp.data_filter DEBUG Watterson()
772690 smcpp.data_filter DEBUG sites: 58131655/14661980076	watterson:0.003965
772697 smcpp.data_filter DEBUG CountMutations(w=163934)
775763 smcpp.data_filter DEBUG mutation counts in 163934bp windows: min=0 .05=0 .95=232 max=642
775790 smcpp.analysis.base DEBUG Creating inference manager...
775791 smcpp.analysis.base DEBUG Creating inference manager for ('LRE', 'Wild')
9665827 smcpp.analysis.base DEBUG Creating inference manager for ('Wild', 'LRE')
terminate called without an active exception
stack trace:
  /lib/x86_64-linux-gnu/libc.so.6 : ()+0x46210
  /lib/x86_64-linux-gnu/libc.so.6 : gsignal()+0xcb
  /lib/x86_64-linux-gnu/libc.so.6 : abort()+0x12b
  /lib/x86_64-linux-gnu/libstdc++.so.6 : ()+0x9e951
  /lib/x86_64-linux-gnu/libstdc++.so.6 : ()+0xaa47c
  /lib/x86_64-linux-gnu/libstdc++.so.6 : ()+0xaa4e7
  /usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/_smcpp.cpython-38-x86_64-linux-gnu.so : ()+0x45508
  /usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/_smcpp.cpython-38-x86_64-linux-gnu.so : NPopInferenceManager<2ul>::construct_bins(double)+0x1168
  /usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/_smcpp.cpython-38-x86_64-linux-gnu.so : NPopInferenceManager<2ul>::NPopInferenceManager(Eigen::Matrix<int, 2, 1, 0, 2, 1>, Eigen::Matrix<int, 2, 1, 0, 2, 1>, std::vector<int, std::allocator<int> >, std::vector<int*, std::allocator<int*> >, std::vector<double, std::allocator<double> >, double, ConditionedSFS<Eigen::AutoDiffScalar<Eigen::Matrix<double, -1, 1, 0, -1, 1> > >*)+0x245
  /usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/_smcpp.cpython-38-x86_64-linux-gnu.so : TwoPopInferenceManager::TwoPopInferenceManager(int, int, int, int, std::vector<int, std::allocator<int> >, std::vector<int*, std::allocator<int*> >, std::vector<double, std::allocator<double> >, double)+0x1fb
  /usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/_smcpp.cpython-38-x86_64-linux-gnu.so : ()+0x5afdb
  /usr/bin/python3() [0x5a67fa]
  /usr/bin/python3 : PyObject_Call()+0x27e
  /usr/bin/python3 : _PyEval_EvalFrameDefault()+0x1f70
  /usr/bin/python3 : _PyFunction_Vectorcall()+0x1b6
  /usr/bin/python3 : _PyEval_EvalFrameDefault()+0x8f6
  /usr/bin/python3 : _PyFunction_Vectorcall()+0x1b6
  /usr/bin/python3() [0x59ba6e]
  /usr/bin/python3 : _PyObject_MakeTpCall()+0x1ff
  /usr/bin/python3 : _PyEval_EvalFrameDefault()+0x598a
  /usr/bin/python3 : _PyFunction_Vectorcall()+0x1b6
  /usr/bin/python3 : _PyEval_EvalFrameDefault()+0x8f6
  /usr/bin/python3 : _PyFunction_Vectorcall()+0x1b6
  /usr/bin/python3 : _PyEval_EvalFrameDefault()+0x71e
  /usr/bin/python3 : _PyEval_EvalCodeWithName()+0x26a
  /usr/bin/python3 : PyEval_EvalCode()+0x27
  /usr/bin/python3() [0x67d5a1]
  /usr/bin/python3() [0x67d61f]
  /usr/bin/python3 : PyRun_FileExFlags()+0x9b
  /usr/bin/python3 : PyRun_SimpleFileExFlags()+0x17e
  /usr/bin/python3 : Py_RunMain()+0x212
  /usr/bin/python3 : Py_BytesMain()+0x2d
  /lib/x86_64-linux-gnu/libc.so.6 : __libc_start_main()+0xf3
  /usr/bin/python3 : _start()+0x2e
/var/spool/slurmd/job9599018/slurm_script: line 19: 83138 Aborted                 singularity run -B /global/scratch2/peter_stokes /global/scratch2/peter_stokes/smcpp_latest.sif split --cores 52 -v -o /global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts /global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/Wild_Knots.final.json /global/scratch2/peter_stokes/DemographicInference/Modeling/smcpp/split/output/pooledOuts/smcPP_Estimate_Landrace_knots.final.json Wild_Landrace_Ann1238_AllReads_Chr01.smc.gz Wild_Landrace_ANN1198_Chr01.smc.gz Wild_Landrace_IA2W-11_Chr01.smc.gz Wild_Landrace_Ann1238_AllReads_Chr13.smc.gz Wild_Landrace_ANN1198_Chr13.smc.gz Wild_Landrace_IA2W-11_Chr13.smc.gz Wild_Landrace_Ann1238_AllReads_Chr15.smc.gz Wild_Landrace_ANN1198_Chr15.smc.gz Wild_Landrace_IA2W-11_Chr15.smc.gz Wild_Landrace_MO1W-33_Chr15.smc.gz Wild_Landrace_ann01_cwIA_Chr15.smc.gz Wild_Landrace_ann04_nwAR_Chr15.smc.gz Wild_Landrace_MO1W-33_Chr13.smc.gz Wild_Landrace_ann01_cwIA_Chr13.smc.gz Wild_Landrace_ann04_nwAR_Chr13.smc.gz Wild_Landrace_MO1W-33_Chr14.smc.gz Wild_Landrace_ann01_cwIA_Chr14.smc.gz Wild_Landrace_ann04_nwAR_Chr14.smc.gz Wild_Landrace_MO1W-33_Chr01.smc.gz Wild_Landrace_ann01_cwIA_Chr01.smc.gz Wild_Landrace_ann04_nwAR_Chr01.smc.gz Wild_Landrace_ann39_ncNE_Chr01.smc.gz Wild_Landrace_ann34_cwKS_Chr01.smc.gz Wild_Landrace_ann10_ccIL_Chr01.smc.gz Wild_Landrace_ann39_ncNE_Chr13.smc.gz Wild_Landrace_ann34_cwKS_Chr13.smc.gz Wild_Landrace_ann10_ccIL_Chr13.smc.gz Wild_Landrace_ann39_ncNE_Chr14.smc.gz Wild_Landrace_ann34_cwKS_Chr14.smc.gz Wild_Landrace_ann10_ccIL_Chr14.smc.gz Wild_Landrace_ann39_ncNE_Chr15.smc.gz Wild_Landrace_ann34_cwKS_Chr15.smc.gz Wild_Landrace_ann10_ccIL_Chr15.smc.gz Landrace_Wild_Arikara_Chr13.smc.gz Landrace_Wild_Hidatsa_Chr13.smc.gz Landrace_Wild_Mandan1_PPN046_Chr13.smc.gz Landrace_Wild_Havasupai_Chr13.smc.gz Landrace_Wild_Laguna_Pueblo_Chr13.smc.gz Landrace_Wild_Hopi_real_NEW_Chr13.smc.gz