Yaamini’s Notebook: WGBS Analysis Part 2

Fixing my bismark script for Mox

I previously submitted my bismark job on Mox, but it remained in the queue. Steven pointed out that my wall time overlapped with routine Mox maintenance, and that I should reduce it so the job finishes (or is terminated) by 9 a.m. on Tuesday. Once I reduced it, I ran into two problems:

  • path_to_bowtie was not recognized
  • Wildcards were not recognized in my find | xargs command

I posted this issue to figure out why this happened. Looking at other bismark scripts Steven posted, I figured out that I could get the script to run if I modified the wildcard, explicity wrote out all program and file paths, and changed from bismark 0.21.0 to bismark 0.19.0. I saved my modified script here and started the job on Mox.

Unfortunately, I couldn’t get one sample finished before maintenance started. Once maintenance is over, I’ll restart my job with a longer wall time. I’m a bit nervous about getting data before PCSGA…we’ll see what happens and if I need to present on C. virginica stuff instead.

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