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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
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Segmentation faultng... | phase_common #26

Open FranjoIM opened 1 year ago

FranjoIM commented 1 year ago 
for i in {22..22};
do
shapeit5 phase_common \
          --input ${WD}/0601/ABCD.chr${i}.vcf.gz \
          --map ${RF}/SHAPEIT5MAPS/chr${i}.b37.gmap.gz \
          --region ${i} \
          --reference ${RF}/1000Gp3hg37/chr${i}.vcf.gz \
          --thread 8 \
          --mcmc-iterations 10b,1p,1b,1p,1b,1p,1b,1p,10m \
          --pbwt-depth 8 \
          --log ${WD}/0602/ABCD.chr${i}.phased.log \
          --output ${WD}/0602/ABCD.chr${i}.phased.xcf \
          --output-format "bh"
done

[SHAPEIT5] phase_common (jointly phase multiple common markers)
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau@gmail.com
  * Version       : 5.1.0 / commit = 744384b / release = 2023-03-31
  * Run date      : 22/04/2023 - 02:39:53

Files:
  * Input         : [/home/fivankov/DRIVE/ABCD/dADHD/0601/ABCD.chr22.vcf.gz]
  * Reference     : [/home/fivankov/DRIVE/ReferenceFiles/1000Gp3hg37/chr22.vcf.gz]
  * Genetic Map   : [/home/fivankov/DRIVE/ReferenceFiles/SHAPEIT5MAPS/chr22.b37.gmap.gz]
  * Output        : [/home/fivankov/DRIVE/ABCD/dADHD/0602/ABCD.chr22.phased.xcf]
  * Output format : [bh]
  * Output LOG    : [/home/fivankov/DRIVE/ABCD/dADHD/0602/ABCD.chr22.phased.log]

Parameters:
  * Seed    : 15052011
  * Threads : 8 threads
  * MCMC    : 27 iterations [10b + 1p + 1b + 1p + 1b + 1p + 1b + 1p + 10m]
  * PBWT    : [window = 4cM / depth = 8 / modulo = 0.1 / mac = 5 / missing = 0.1]
  * HMM     : [window = 4cM / Ne = 15000 / Recombination rates given by genetic map]

Reading genotype data:
Segmentation faultng ...
odelaneau commented 1 year ago

To diagnose this; I will need example files reproducing the error.

Can you send this to @.*** ?

Thanks;

Olivier Delaneau

http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail Sans virus.www.avg.com http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

Le sam. 22 avr. 2023 à 04:40, Franjo Ivankovic @.***> a écrit :

`for i in {22..22}; do shapeit5 phase_common --input ${WD}/0601/ABCD.chr${i}.vcf.gz --map ${RF}/SHAPEIT5MAPS/chr${i}.b37.gmap.gz --region ${i} --reference ${RF}/1000Gp3hg37/chr${i}.vcf.gz --thread 8 --mcmc-iterations 10b,1p,1b,1p,1b,1p,1b,1p,10m --pbwt-depth 8 --log ${WD}/0602/ABCD.chr${i}.phased.log --output ${WD}/0602/ABCD.chr${i}.phased.xcf --output-format "bh" done

[SHAPEIT5] phase_common (jointly phase multiple common markers)

Files:

  • Input : [/home/fivankov/DRIVE/ABCD/dADHD/0601/ABCD.chr22.vcf.gz]
  • Reference : [/home/fivankov/DRIVE/ReferenceFiles/1000Gp3hg37/chr22.vcf.gz]
  • Genetic Map : [/home/fivankov/DRIVE/ReferenceFiles/SHAPEIT5MAPS/chr22.b37.gmap.gz]
  • Output : [/home/fivankov/DRIVE/ABCD/dADHD/0602/ABCD.chr22.phased.xcf]
  • Output format : [bh]
  • Output LOG : [/home/fivankov/DRIVE/ABCD/dADHD/0602/ABCD.chr22.phased.log]

Parameters:

  • Seed : 15052011
  • Threads : 8 threads
  • MCMC : 27 iterations [10b + 1p + 1b + 1p + 1b + 1p + 1b + 1p + 10m]
  • PBWT : [window = 4cM / depth = 8 / modulo = 0.1 / mac = 5 / missing = 0.1]
  • HMM : [window = 4cM / Ne = 15000 / Recombination rates given by genetic map]

Reading genotype data: Segmentation faultng ...`

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odelaneau commented 1 year ago

Arf, email addresses do not go through. Anyway; the email address is in the software verbose header.

odelaneau commented 1 year ago

Hi,

Could you check if the v5.1.1 pre-release fixes your problem?

Best,