API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit

[lily616]

Hello, I have a question about running the nextwork, could you give me a suggestion?

The code as the following,

Singularity> nextflow run nextflow/variant_call.nf --ref_dir /tmp/singularity-3.8.0/refrence/ --reads_in1 /tmp/singularity-3.8.0/diyData/1.L350_BDMS190036238-1a_1.fq.clean.gz --reads_in2 /tmp/singularity-3.8.0/diyData/1.L350_BDMS190036238-1a_2.fq.clean.gz --output_dir result --sample_name sample

The output:
N E X T F L O W ~ version 21.10.0
Pulling nextflow-io/nextflow ...
API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit

The environment

• Nextflow version: version 21.10.0.5640
• Java version: 17.0.1
• Operating system: Linux

I have confused me some time, I would grateful for you if you can help me, thank you.

[FriederikeHanssen]

After just running into this myself again and forgetting how to do this:

If you use the Github CLI you should be able to gh auth login to set it up.

[Luke-ebbis]

How did you end up solving this? I have the same issue after logging in with gh.

$ nextflow pull nf-core/ampliseq 
Checking nf-core/ampliseq ...
API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit

$ gh auth status
github.com
  ✓ Logged in to github.com account Luke-ebbis (/home/bakke333/.config/gh/hosts.yml)
  - Active account: true
  - Git operations protocol: https
  - Token: github_pat_11AW********OsQ4UtbXd77C_***********************************************************

[wvnicholson]

I'm getting the same problem. Also after logging in with gh:

./eg_22_3_run_assemblebac.sh |& tee eg_22_3_run_assemblebac_errs6.out

N E X T F L O W ~ version 24.10.4

Pulling avantonder/assembleBAC ...
WARN: Cannot read project manifest -- Cause: API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit
API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit
(nextflow_upgrade) [[email protected]@smedmaster01 S_aureus]$ gh auth status
github.com
✓ Logged in to github.com account wvnicholson (/home/phe.gov.uk/william.v.nicholson/.config/gh/hosts.yml)

• Active account: true
• Git operations protocol: ssh
• Token: ghp_************************************
• Token scopes: 'read:org', 'repo'
  (nextflow_upgrade) [[email protected]@smedmaster01 S_aureus]

Contents of the shell script are just this command (plus some comments and "exit 0" at the end):

nextflow run avantonder/assembleBAC
-r main
-resume -profile singularity
--max_memory '16.GB' --max_cpus 8
--input samplesheet.csv
--outdir results/assemblebac
--baktadb databases/bakta_light_20240119
--genome_size 2.8M
--checkm2db databases/checkm2_v2_20210323/uniref100.KO.1.dmnd

[wvnicholson]

It's looking like your authentication information may need to be in a config file usually $HOME/.nexflow/scm according to the documentation at https://www.nextflow.io/docs/latest/git.html#git-configuration . (It looks like this is what allowed my relevant job to eventually finish although I did have to restart it, taking advantage of the "-resume" option. On the first run it soon looked like it had got past the part where it pulls stuff from GitHub.) It isn't clear if the thing with "gh auth login" is either necessary or sufficient since Nextflow may re-authenticate itself anyway (chucking away anything obtained with "gh auth login"). Not sure why none of the experts have weighed in to mention the config file in the past four years.