Open FranjoIM opened 1 year ago
To diagnose this; I will need example files reproducing the error.
Can you send this to @.*** ?
Thanks;
Olivier Delaneau
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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)
- Author : Olivier DELANEAU, University of Lausanne
- Contact : @.***
- Version : 5.1.0 / commit = 744384b https://github.com/odelaneau/shapeit5/commit/744384bb7ffb59dc9570add5c70cd88c8c228510 / 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 ...`
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Arf, email addresses do not go through. Anyway; the email address is in the software verbose header.
Hi,
Could you check if the v5.1.1 pre-release fixes your problem?
Best,