Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Gzipped files get cutoff when loading from google cloud #1579

Open
lbergelson opened this issue Sep 24, 2024 · 1 comment
Open

Gzipped files get cutoff when loading from google cloud #1579

lbergelson opened this issue Sep 24, 2024 · 1 comment

Comments

@lbergelson
Copy link
Contributor

bed.gz files are sometimes incompletely loaded when accessing them from google cloud.

It's unclear what set of conditions causes this to happen, but it seems to be deterministic and repeatable.

image

Strangely, copying the same file to a public google bucket caused it to load correctly. There is no error message or obvious sign that something went wrong when loading, the file just gets cutoff at chromosome 10.

The user reports that they've seen similar things with other files including gzipped vcf.
@lbergelson
Copy link
Contributor Author

This is caused by samtools/htsjdk#1691.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@lbergelson