Juicer: SLURM_JOB_ID: invalid indirect expansion [error]

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George Bell

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Jul 28, 2025, 7:44:12 PMJul 28
to 3D Genomics
We're running juicer 1.6 using the slurm version of juicer.sh
We kept getting an error like 
juicer.sh: line ____: SLURM_JOB_ID: invalid indirect expansion

This caused problems with creation of the the split_rmdups.awk slurm script, so that step wasn't run, and the pipeline couldn't finish.

In our case, the solution was to remove the juicer.sh line (actually just a comment for the output slurm script) that mentions SLURM_JOB_ID.

We might have been doing something wrong that led to this error, but if not, our solution might be helpful for others.
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