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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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core dumped at genotype_reader2.cpp:127 #38

Open verne91 opened 3 years ago

verne91 commented 3 years ago

Hi, I am using shapeit4 but there is a core dumped error during the initialization.

The error log is:

SHAPEIT
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau@gmail.com
  * Version       : 4.1.3
  * Run date      : 28/10/2020 - 23:41:08

Files:
  * Input VCF     : [22.snps.VQSR.vcf.gz]
  * Reference VCF : [HRC.r1-1.GRCh37.wgs.mac5.sites.bcf]
  * Genetic Map   : [chr22.b37.gmap.gz]
  * Output VCF    : [22.phased.vcf]
  * Output LOG    : [22.phased.log]

Parameters:
  * Seed    : 15052011
  * Threads : 4 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=0.02 cM]
  * HMM     : K is variable / min W is 2.50cM / Ne is 15000
  * HMM     : Recombination rates given by genetic map
  * HMM     : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001
  * HMM     : !AVX2 optimization inactive!
  * IBD2    : length>=3.00cM [N>=150 / MAF>=0.010 / MDR<=0.500]

Initialization:
  * VCF/BCF scanning [Nm=2 / Nr=0 / L=39458 / Reg=22] (1.02s)
shapeit4: src/io/genotype_reader2.cpp:127: void genotype_reader::readGenotypes1(std::string, std::string): Assertion `ngt_ref == 2 * n_ref_samples' faile d.
Aborted (core dumped)
odelaneau commented 3 years ago

Hi,

Given the log file, it seems that the software cannot find samples in the reference panel (Nr = 0, which is not what we expect for HRC). Double check your files as we successfully run S4 on HRC in the past.

Best,

Olivier.