search

odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
89 stars 17 forks source link

ERROR: Could not find conditioning haplotypes #19

Open weishwu opened 4 years ago

weishwu commented 4 years ago

Shapeit4 gave me an error on one chromosome:

ERROR: Could not find conditioning haplotypes for [sample_137739] / check options --pbwt- and --ibd2-

shapeit4 --input DNA.phased.chr3.bcf --map chr3.b38.gmap.gz --region chr3 --output DNA.shapeit4phased.chr3.vcf --use-PS 0.0001 --sequencing --scaffold DNA.phased.chr3.trios.bcf

How should I change the pbwt and idb2 parameters?

weishwu commented 4 years ago

I got this error for every sample but it only happened to chr3. Any help?

odelaneau commented 4 years ago

Could you please send the log files on olivier.delaneau@gmail.com? So that I can have a look.

Best,

weishwu commented 4 years ago

SHAPEIT

  • Author : Olivier DELANEAU, University of Lausanne
  • Contact : olivier.delaneau@gmail.com
  • Version : 4.1.2
  • Run date : 04/03/2020 - 20:18:45

Files:

  • Input VCF : [DNA.phased.chr3.bcf]
  • Scaffold VCF : [DNA.phased.chr3.trios.bcf]
  • Genetic Map : [chr3.b38.gmap.gz]
  • Output VCF : [DNA.shapeit4phased.chr3.vcf]

Parameters:

  • Seed : 15052011
  • Threads : 1 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 : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001
  • HMM : AVX2 optimization active
  • IBD2 : length>=3.00cM [N>=10000 / MAF>=0.000 / MDR<=0.500]

Initialization:

  • VCF/BCF scanning [N=623 / L=2644 / Reg=chr3] (0.09s)
  • VCF/BCF parsing [Hom=44.3% / Het=4.9% / Pha=1.919% / Sca=1.688% / Mis=50.8%] (0.25s)
  • GMAP parsing [n=223321] (0.17s)
  • cM interpolation [s=294 / i=2350] (0.00s)
  • PBWT indexing [l=347] (0.00s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)
  • IBD2 constraints [#inds=0 / #pairs=0] (0.02s)
  • PBWT phase sweep (0.10s)
  • Build genotype graphs [seg=19096] (0.03s)

Burn-in iteration [1/5]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.00s)
  • HMM computations [K=67.9+/-37.0 / W=42.96Mb] (3.20s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)

Burn-in iteration [2/5]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.01s)
  • HMM computations [K=64.3+/-36.3 / W=42.91Mb] (3.11s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)

Burn-in iteration [3/5]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.01s)
  • HMM computations [K=61.2+/-35.4 / W=43.08Mb] (2.96s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)

Burn-in iteration [4/5]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.01s)
  • HMM computations [K=58.4+/-34.0 / W=43.17Mb] (2.86s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)

Burn-in iteration [5/5]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.01s)
  • HMM computations [K=58.7+/-32.9 / W=43.00Mb] (2.79s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)

Pruning iteration [1/1]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.01s)
  • HMM computations [K=57.8+/-33.5 / W=43.47Mb] (2.98s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)
  • Trimming [pc=38.29%]

Burn-in iteration [1/1]

  • V2H transpose (0.00s)
  • PBWT selection (0.03s)
  • C2H transpose (0.00s)
  • HMM computations [0%] ERROR: Could not find conditioning haplotypes for [sample_138] / check options --pbwt- and --ibd2-
weishwu commented 4 years ago

Sorry I forgot that you wanted me to send it to your email. The complete log was pasted above. I guess this works? By the way, this error message was emitted when I was trying to phase about 5 samples. In my latest run where I gave Shapeit4 400 samples, there was no error.

santiago1234 commented 3 years ago

Hi,

I am curious if a solution for this has been found, I am getting the same error. I am using version 4.2.0 thanks in advance!

LindoNkambule commented 2 years ago

Hi,

I am also getting the same error using version 4.2.2. Is there a solution for this? I have also attached the log file. shapeit4.phase.log

@santiago1234 did you end up finding a solution?

santiago1234 commented 2 years ago

Hi @LindoNkambule , no I did not :( .

rrlove commented 2 years ago

I'm getting this error (using version 4.2.2) in every window while attempting to phase a genome in 10 Mb windows. It's not always the same specimens giving the error, but it's generally the specimens closer to the beginning of the sample list. I've tried with the default pbwt-depth setting, as well as with "--pbwt-depth 8." The conditioning haplotypes error is often followed by a segmentation fault.

I'm going to try some other phasing software as well, but wanted to add to this thread in case there's any chance of a fix for this issue.

vicbp1 commented 2 years ago

Hi all, I have had the same error. In my case, I ran succesfully for a first dataset with low density. My problems started by increasing the density and even when increase the RAM it resulted in the same error of "Could not find conditioning haplotypes". I obtained a successfull run by adding the --sequencing flag for the version 4.1.2. Have you try that? I hope this can be useful for someone

dralhindi commented 5 months ago

Hey, I've been having the same problem with no luck. I've used the --sequencing flag despite being array data, just to see if things might run. I've having this error occur on every chromosome. Did anyone find a solution?