The genotype imputation in Beagle always stop on specific step and can not finish the imputation file

Question

[r00628112]

Hello~

About the genotype imputation in Beagle, I run the vcf file, but the program always stopped in this step as the attached link.(https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6)

I used this command:

java -jar beagle.25Nov19.28d.jar  gt=200212-NiNK_newPmgenomeDP5Q10maf0.2missing0.5.recode.vcf out=Imput_200212-NiNK_newPmgenomeDP5Q10maf0.2missing0.5.recode

Could anyone give me some suggestions?

Thank you very much

Screen figure

https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6

[Fabio Marroni]

The window in which beagle gets stucked is only one bp long, while others are several kb. Can you give a look at the input file in the position in which beagle gets stucked? Maybe there is something strange there...

[r00628112]

Sure. Thank you so much. (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bHWom4I_ztD5wTMNti9bHvFwRa6eaz8Z (2)The stop site in the beagle imputation file https://drive.google.com/open?id=1RFnAY3ljjykRmibkl7cmz5z4RL-cvAXK

[Fatima]

These links might help:

BEAGLE 4.1 imputation ending short with "at dag.MergeableDag" message

https://faculty.washington.edu/browning/beagle/beagle_5.0_14May18.pdf

Are there NaN's in your data?

[r00628112]

Hi~ Thanks to your reply. I checked the vcf file, and there are no any NaN characters. Then, I followed the solution from the link (add -Xss5m), but it is no work. Thank you very much :D

[Kevin Blighe]

Which error messages are appearing? Can you reply to Fabio's comment, please?

[r00628112]

Ok. Thank you. There are no error message, but an WARNING message showed during processing. (in this photo https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6) And the stop site information are as below: (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bHWom4I_ztD5wTMNti9bHvFwRa6eaz8Z (2)The stop site in the beagle imputation file https://drive.google.com/open?id=1RFnAY3ljjykRmibkl7cmz5z4RL-cvAXK

[Fabio Marroni]

Mmmm, it looks like the entire chromosome contains only one SNP. Is it correct? Maybe Beagle is not ready to deal with chromosomes/regions with only one SNP. Maybe this is the issue?

BTW, it looks like the link to the warning message is broken.

Answer 1

[Isis]

Hello,

Please check if you have alleles in your file that is not a sequence of A, C, T, G, or N characters. Perhaps you can find some D/I aleles.

Hope to help!