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cbirdlab / charybdis

Metabarcoding Pipeline
GNU General Public License v3.0
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progress reporting #26

Open cbird808 opened 4 years ago

cbird808 commented 4 years ago

now that the module load errors are fixed, it's much more difficult to figure out what is happening. It would be nice to be able to print more information to the screen. I noticed that the echos in the scripts go into the ether. is there a way to recover those?

ekrell commented 4 years ago

Some content like the R scripts and various obitool errors make it through, but not echoes. I don't know why. I will set up a smaller test script and see what I can do.

cbird808 commented 4 years ago

Here is a hackish way to make the echos work:

ekrell commented 4 years ago

I know why now. Whenever I call an SBATCH, I grep the output for only the job ID so that I can stall the next job until the job is done. But grepping means all the other STDOUT is gone. But STDERR makes it through.