search

zhanxw / rvtests

Rare variant test software for next generation sequencing data
134 stars 42 forks source link

vcf2kinship not finding samples in pedigree #13

Closed padlocke11180 closed 7 years ago

padlocke11180 commented 7 years ago

The latest update (20161018) available here, now sends an error when trying to generate kinship while including the ped file.

When running the following command: ../executable/vcf2kinship --inVcf example.vcf.gz --ped pheno --bn --xHemi --out example.output Exclude [ 500 ] samples from VCF files because they do not exist in pedigree file or do not have sex [ERROR] No samples left for analysis, aborting...

Earlier versions of the software did not have this problem.

zhanxw commented 7 years ago

Can you please tell me more about the problem:

Did you use the binary version or compile form the source-codes? Which Linux distribution do you use?

Thanks.

padlocke11180 commented 7 years ago

Hi Xiaowei, It's Adam formerly of Michigan.

I downloaded the compiled binaries on Friday. My Linux version is: 3.0.0-16-server GNU/Linux, but it appears to be independent of linux as numerous collaborators have recently encountered the same problem.

As I think I stated in the original post, this error seems to have cropped up in the most recent version of the software. Older versions all seemed to work fine.

Please let me know if you need anything else.

Adam

On Mon, Feb 6, 2017 at 2:51 AM, zhanxw notifications@github.com wrote:

Can you please tell me more about the problem:

Did you use the binary version or compile form the source-codes? Which Linux distribution do you use?

Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/13#issuecomment-277618477, or mute the thread https://github.com/notifications/unsubscribe-auth/AYXuDzqc5Sflw-jfgkC0qG7zifPIY7neks5rZt8rgaJpZM4L3QXq .

zhanxw commented 7 years ago

Hi Adam,

Thanks very much for the information. I have identified the bug, and will release a new version to fix it.

Best, Xiaowei

zhanxw commented 7 years ago

This release provides the fix: https://github.com/zhanxw/rvtests/releases/tag/v2.0.1

Thanks!

padlocke11180 commented 7 years ago

FYI, you did not update the version information/dates in the new version. may be confusing for some.

Looks like the problem is fixed, though.

Thanks!

On Fri, Feb 10, 2017 at 2:15 AM, zhanxw notifications@github.com wrote:

This release provides the fix: https://github.com/zhanxw/ rvtests/releases/tag/v2.0.1

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/13#issuecomment-278883588, or mute the thread https://github.com/notifications/unsubscribe-auth/AYXuDy1Xapa-7aWORArVqtQJxHsUGRLSks5rbByigaJpZM4L3QXq .

zhanxw commented 7 years ago

I have fixed the version information/dates in the new version.

Thank you very much. Xiaowei

On Fri, Feb 10, 2017 at 3:06 PM, padlocke11180 notifications@github.com wrote:

FYI, you did not update the version information/dates in the new version. may be confusing for some.

Looks like the problem is fixed, though.

Thanks!

On Fri, Feb 10, 2017 at 2:15 AM, zhanxw notifications@github.com wrote:

This release provides the fix: https://github.com/zhanxw/ rvtests/releases/tag/v2.0.1

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/13#issuecomment-278883588, or mute the thread https://github.com/notifications/unsubscribe-auth/AYXuDy1Xapa- 7aWORArVqtQJxHsUGRLSks5rbByigaJpZM4L3QXq .

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/13#issuecomment-279065807, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJoiGUuY6G43V2wb1_xXoXy1IHJ7ks9ks5rbNFigaJpZM4L3QXq .