Multiple errors running pipeline

[gjacobsen15]

Hello,

Thank you for making this pipeline available. I was able to install and start a run on my data (just using 2 paired-end samples at first, please let me know if the pipeline requires more than 2 samples). I have run into a few errors but have been able to fix them with simple syntax changes. However, I am now running into two errors that I'm not sure how to fix.
The first is during the "#DEG & Annotation...":

Still, it is able to halt this and keep running. The second error is then a "file not found" error so I'm assuming something upstream didn't work.

I do not have a computer science background but my colleagues in CS have also been unable to debug. They told me they ran into similar errors using the test run files as well. I appreciate any input!

Thanks,
Gillian