ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObjec

[TheBorgy]

I pip installed the program as suggested. Attempting to run test data in this repository generated the following error
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObjec

[giovanniquinones]

Please update your numpy version.
If the error persists, please provide the full command and bam file you are using to reproduce the error.

[alaminzju]

After updating numpy version, I got another error "ImportError: cannot import name 'Reader' from 'parser'". This problem was solved by running conda install --channel "conda-forge" pyvcf.

[giovanniquinones]

Thank you for sharing.
I realize it will help to share a docker/singularity image given the many dependencies-related issues.
Will work on that and share it soon enough.

[giovanniquinones]

singularity container uploaded

[JiangyanYu]

Thanks for sharing the singularity image. Unfortunately when I pull the image, I received the 401 unauthorized error. Details of the errors are below:

FATAL: While pulling library image: error fetching image: request did not succeed: UNAUTHORIZED: unauthorized to access repository: giovas/collection/s5, action: pull: unauthorized to access repository: giovas/collection/s5, action: pull (401 Unauthorized)

[giovanniquinones]

Thanks for bringing this to my attention.
Please refer to this link: sylabs/singularity#515
It seems you need to login first before trying to pull the image.
Please let me know if that works for you.

[JiangyanYu]

Thanks for the quick response! I have tried remote login with token generated from cloud.sylabs.io, unfortunately the error persists (see below). By the way I looked for the image in cloud.sylabs.io libraries but could not find any items. Is it not pushed or is it private? Thanks!

$ singularity remote login --username jiangyanyu
Generate an access token at https://cloud.sylabs.io/auth/tokens, and paste it here.
Token entered will be hidden for security.
Access Token:
INFO: Access Token Verified!

$ singularity remote list
Cloud Services Endpoints
NAME URI ACTIVE GLOBAL EXCLUSIVE INSECURE
SylabsCloud cloud.sylabs.io YES YES NO NO
Keyservers
URI GLOBAL INSECURE ORDER
https://keys.sylabs.io YES NO 1*
Active cloud services keyserver

$ singularity pull library://giovas/collection/s5
FATAL: While pulling library image: error fetching image: request did not succeed: UNAUTHORIZED: unauthorized to access repository: giovas/collection/s5, action: pull: unauthorized to access repository: giovas/collection/s5, action: pull (401 Unauthorized)

[giovanniquinones]

The repository was private. I apologize for the inconvenience. I made it public now.

[JiangyanYu]

Thanks! Now I am able to pull the image without remote login.