Closed IHautaI closed 5 years ago
When you clone the repo locally, I assume you are logged in with your Github? It could be that there is some default quota, and as an anonymous user you exceed it on this clone. I am in the middle of traveling but I'll take a look at this as soon as I get back to my computer! As a sanity check try doing the clone where you are an anonymous user.
Ah, looking at the log I think it's likely you ran out of disk space. How big is the entire download?
Thanks for the quick response! I'm checking on the anonymous user build right now. The final size of the image is 2.6G, not sure on how big the GATK clone is when building.
It doesn't appear to be github login. Total gatk size was around 890M after git-lfs ran.
Okay, it looks like the error code is 429:
429 - The user has hit a rate limit with the server. Though the API does not specify any rate limits, implementors are encouraged to set some for availability reasons.
And there is this additional (unrelated?) error:
debconf: delaying package configuration, since apt-utils is not installed
E: Can not write log (Is /dev/pts mounted?) - posix_openpt (2: No such file or directory)
The other thing that sticks out is the "smudge error" and I've never seen this before (albeit I don't use LFS). I would try various ways of doing the checkout, or adding debug/trace to using lfs?
https://github.com/git-lfs/git-lfs/issues/2652
You could also try getting the files another way?
Do you still have an issue here? Closing, as this is an issue with git-lfs.
Link to Container Collection Log, Build, or Collection (in that order)
Building a container with everything necessary for the GATK4 preprocessing pipeline ( in SCIF, as opposed to their docker image ) for use with nextflow
https://www.singularity-hub.org/containers/2801/log
Behavior when Building Locally
Builds just fine locally.
Error on Singularity Hub
git-lfs rate limit exceeded ( near bottom of the log ).
What do you think is going on?
No idea. Not sure why it would exceed the rate limit on singularity-hub but not locally.
I'm doing the localJar build and I'm not pulling the test files, just the ones necessary for building: https://github.com/broadinstitute/gatk#building