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March 19, 2021 23:37
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SHAPEIT4.1.3 chromosome X failure
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| SHAPEIT | |
| * Author : Olivier DELANEAU, University of Lausanne | |
| * Contact : olivier.delaneau@gmail.com | |
| * Version : 4.1.2 | |
| * Run date : 19/03/2021 - 18:30:15 | |
| Files: | |
| * Input VCF : [CCDG_13607_B01_GRM_WGS_2019-02-19_chrX.recalibrated_variants.vcf.gz] | |
| * Genetic Map : [chrX.b38.gmap.gz] | |
| * Output VCF : [phased_1kgp_gatk_chrX.vcf.gz] | |
| * Output LOG : [gatk_shapeit413_chrX.txt] | |
| Parameters: | |
| * Seed : 15052011 | |
| * Threads : 96 threads | |
| * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] | |
| * PBWT : Depth of PBWT neighbours to condition on: 4 | |
| * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.0005 cM] | |
| * HMM : K is variable / min W is 2.50cM / Ne is 15000 | |
| * HMM : Recombination rates given by genetic map | |
| * HMM : AVX2 optimization active | |
| * IBD2 : length>=3.00cM [N>=10000 / MAF>=0.000 / MDR<=0.500] | |
| Initialization: | |
| * VCF/BCF scanning [N=2504 / L=4551358 / Reg=chrX] (5366.06s) | |
| * VCF/BCF parsing [Hom=98.2% / Het=1.0% / Mis=0.8%] (5603.05s) | |
| * GMAP parsing [n=89236] (0.09s) | |
| * cM interpolation [s=86432 / i=4464926] (0.37s) | |
| * PBWT indexing [l=229920] (0.31s) | |
| * HAP update (88.75s) | |
| * H2V transpose (58.95s) | |
| * IBD2 constraints [#inds=2 / #pairs=2] (192.88s) | |
| * PBWT phase sweep (670.83s) | |
| * Build genotype graphs [seg=39202378] (3.70s) | |
| Burn-in iteration [1/5] | |
| * V2H transpose (32.31s) | |
| * PBWT selection (105.06s) | |
| * C2H transpose (23.64s) |
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