issue with pulling from GitHub on raven

[grace-ac]

before i commit, i tried pulling while in Raven and got this error:

/usr/bin/git pull fatal: update_ref failed for ref 'ORIG_HEAD': could not write to '.git/ORIG_HEAD'

anyone know what this means? how do i fix?

[sr320]

what repo? can you provide a screenshot?

[grace-ac]

repo: https://github.com/grace-ac/paper-pycno-sswd-2021-2022

i just tried to pull again and got a different message:

[kubu4]

You may want to see if you have the file .git/ORIG_HEAD.lock

If you have that, delete that lock file (rm .git/ORIG_HEAD.lock) , then try to pull. If pulling fails again with that same error message, then delete .git/ORIG_HEAD

rm .git/ORIG_HEAD

[kubu4]

My comment above is in response to your original post. Not sure what to do regarding your subsequent post.

[kubu4]

The new error message suggests that the main branch was removed from the remote repo (i.e. removed from your repo GitHub.com).

Try running this in a Terminal (in that git repo) and let us know what it says:

git ls-remote origin

[grace-ac]

Graces-MacBook-Air-10:paper-pycno-sswd-2021-2022 graciecrandall$ git ls-remote origin
6f9a2e3a19851c7269c933603f6149b651a292da    HEAD
6f9a2e3a19851c7269c933603f6149b651a292da    refs/heads/main

[kubu4]

But, honestly, with stuff like this, it's probably easier to copy the documents you've made changes to, to another location on the computer, then nuke your local copy of the problematic repo, and then re-clone the repo.

Then, copy your the docs back over to the freshly-cloned repo....

[grace-ac]

ok!

i don't get how this happened in the first place? I usually am pretty good about pulling before committing and pushing.

[kubu4]

Also, any possibility that the HDD is full???? That's a common cause of weird problems with various programs...

Which HDD are you using?

[grace-ac]

Wouldn't have thought to check that!

I'm using 8TB_HDD_02

[sr320]

/dev/sdd1       7.3T  6.9T  898M 100% /home/shared/8TB_HDD_02
/dev/sdb1       7.3T  4.4T  2.6T  64% /home/shared/8TB_HDD_03

full?

[kubu4]

Yep, that's the issue!

[grace-ac]

ok yay! i'm sure i have tons of stuff i can remove... i'll look through that this evening after my meetings and tomorrow morning

[kubu4]

The sooner you can tackle this, the better. Everyone uses that drive and, as long as it's full, no one else will be able to run any analysis.

[grace-ac]

got it!! i'll get it going after my meetings. hopefully they'll wrap up quick

[kubu4]

Thanks!

[grace-ac]

is it a bad idea to delete files that were used to create count matrices?

as an example:

graceac9@raven:~/GitHub/paper-pycno-sswd-2021-2022/analyses/03-kallisto$ ls
kallisto_20240118.isoform.counts.matrix                PSC-36  PSC-52  PSC-67
kallisto_20240118.isoform.TMM.EXPR.matrix              PSC-37  PSC-54  PSC-69
kallisto_20240118.isoform.TPM.not_cross_norm           PSC-38  PSC-56  PSC-71
kallisto_20240118.isoform.TPM.not_cross_norm.runTMM.R  PSC-39  PSC-57  PSC-73
PSC-19                                                 PSC-40  PSC-58  PSC-75
PSC-23                                                 PSC-42  PSC-59  PSC-76
PSC-24                                                 PSC-43  PSC-61  PSC-78
PSC-34                                                 PSC-48  PSC-63  PSC-81
PSC-35                                                 PSC-49  PSC-64  PSC-83

each of those PSC-## is a folder that contains files abundance.h5 abundance.tsv run_info.json

[kubu4]

Don't know, but you want to delete LARGE files (like SAMs, BAMs, FastQs).

[grace-ac]

the space was the issue! all working now and i'll keep deleting stuff that's not needed