Failed to download forest somatic.v0.7.4.forest.gz

Question

Failed to download forest somatic.v0.7.4.forest.gz

Axze-rgb opened this issue a year ago · comments

Axze-rgb commented a year ago

Hello,

the title is pretty self-explanatory. The command

/install.py --dependencies --forests failed.

Is there an issue with the cloud storage, such as it has moved, is not paid for any more, etc?

Thanks!

EDIT2: seems to be a billing issue on the Google cloud

Daniel Cooke · Answer 1 · Thu Jul 13 2023 05:42:10 GMT+0800 (China Standard Time)

Hi, Sorry it's taken so long to address this - there was a billing problem with my Google Cloud account. I'll look to move the files over to Zenodo as suggested in #261 asap.

Gennaro Gambardella · Answer 2 · Fri Jul 14 2023 23:31:36 GMT+0800 (China Standard Time)

An other free solution were you can put useful files is figshare or github with LFS (max file dimension is 2GB with the free plan)

Axze-rgb · Answer 3 · Sat Jul 15 2023 16:19:22 GMT+0800 (China Standard Time)

Tanks Dan for taking the time to fix this. Octopus is an awesome tool! we need it.

Axze-rgb · Answer 4 · Tue Jul 25 2023 15:54:24 GMT+0800 (China Standard Time)

Hello

do you have an idea about when this will be fixed? If I (and the community) can help, please let us know. Octopus is an awesome SNP callers, we must preserve it! Thank you

Daniel Cooke · Answer 5 · Mon Aug 14 2023 05:02:33 GMT+0800 (China Standard Time)

I've added the forest files to the repo with LFS.

Axze-rgb · Answer 6 · Wed Sep 13 2023 15:31:41 GMT+0800 (China Standard Time)

is it normal the files ends in .gz but are NOT compressed? Also, upon inspection they look like HTML files but I don't see where are the decisions. I am no expert though, but could you kindly double check you haven't uploaded the wrong file? Which would explain while all my call returns empty vcf. Thanks

Jean Elbers · Answer 7 · Wed Sep 13 2023 16:03:58 GMT+0800 (China Standard Time)

I think maybe you are trying to download the pointers to the files as they were uploaded with git lfs.

As far as I know, you need to do the following, but note the error message at the bottom

git clone https://github.com/luntergroup/octopus
cd octopus/
# you need to install git-lfs
git lfs pull

batch response: This repository is over its data quota. Account responsible for LFS bandwidth should purchase more data packs to restore access.                                               
Failed to fetch some objects from 'https://github.com/luntergroup/octopus.git/info/lfs'

So, nothing more can be done until the data quota is increased or perhaps refreshes (not sure if it is a monthly thing?)

Axze-rgb · Answer 8 · Wed Sep 13 2023 18:41:53 GMT+0800 (China Standard Time)

Oh, ok, thanks, so we still don't have the forest files available.

git lfs pull returns nothing for me

EDIT: ok for an unknown reason I had to redownload the repo. And I have the same error message as you.

@dancooke Is there a way we can help you? Maybe Zenodo can be a solution?
https://zenodo.org/ (I am not involved with zenodo I have no conflict of interest).