"segmentation fault" using spitted vcf files

[liangjiaoxue]

Hi Peter,
I am trying to split one large vcf file into smaller files so that I could run the jobs parallelly. I always get the "segmentation fault" error for some of the small files(7 of 22 total files). However, the HapCUT2 works well on the original file.
Could you please give some suggestion to fix this? Thanks!

Liangjiao

[nh13]

Could you post an example invocation and an original file to debug?

[liangjiaoxue]

Here it the command line:
module load hapcut2
HAPCUT2 --fragments fragment_two_Chr01_P22.txt
--vcf P717_Chr01_part_P22.vcf
--output haplotype_Chr01_22.txt 1>Chr01_22_log.txt 2>Chr01_22_err.txt

The (zipped) input files are here
(deleted)

Thanks

[liangjiaoxue]

Hello Peter,
Please hold this issue. There is an error in the VCF file at the junction between headlines and content lines.
I will rerun the jobs and let you know whether the problem will be gone. Sorry for the confusing information.

[nh13]

@liangjiaoxue not Peter, but good luck!

[pjedge]

Hi Liangjiao, Alright. Let me know if the issue persists afterwards and I'll get right on it. Peter

…

On Fri, Jan 27, 2017, 11:33 AM Nils Homer ***@***.***> wrote: @liangjiaoxue <https://github.com/liangjiaoxue> not Peter, but good luck! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGga6FjJet4tY07-ed_SfAWHGYqnUcE3ks5rWkaXgaJpZM4LwAUm> .

[liangjiaoxue]

Hello Nils and Peter,

I think I can repeat the error now. This was caused by an error in the VCF file. If there is no "\n" at the end of the last line (as in my manually generated testing file), HapCUT2 will report "segmentation fault".
Thank you for writing this great tool for haplotype assembly.
Best,

Liangjiao