Error Message: "No such file or directory found: 'java': 'java'"

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

BSD 3-Clause "New" or "Revised" License

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Error Message: "No such file or directory found: 'java': 'java'" #149

Closed astephen333 closed 2 years ago

astephen333 commented 2 years ago

Tried to run the pipeline on the test case in the Github and the above error message popped up. I also noticed that the previous analysis always says skipped due to md5_match, rather than the usual started. done. message. Attached is a picture of my terminal.

This is on a Linux cluster that has slurm with v2.1.3.

leepc12 commented 2 years ago

It looks like that you don't have java on your system

$ java -version

This pipeline is no longer maintained. Please use https://github.com/ENCODE-DCC/atac-seq-pipeline instead.

astephen333 commented 2 years ago

So sorry, this issue was for the atac-seq-pipeline from ENCODE-DCC. I'll look into your comment and repost if necessary.