Grace’s Notebook: Sent BLAST to Mox, and Plan for rest of Week

I sent a .sh to Mox to perform a BLAST with my assembled C. bairdi transcriptome and swiss prot. I am also working on figuring out how to do this on Hummingbird (on toaster/grace). Additionally, I have come up with a list of things I want to accomplish this week!

BLAST to Mox

Yesterday I wasted a bunch of time trying to figure out how to run Jupyter on Mox in order to perform a BLAST… totally forgot that you can just do: sbatch -p srlab -A srlab shell.script while logged in to Mox…

So today, I got some assistance from Steven and Sam to make sure that my will work (GitHub Issue # 470).

Script lives on Mox in /gscratch/srlab/graceac9/jobs/ and also a copy of it is here.

The job is officially in queue (# 428276).

Plan for the rest of the week (non-class-related tasks):


  • Run Bioanalyzer on what I extracted last week using the Qiagen RNeasy Micro Plus Kit
  • Get input from Emma on my error rate determination of her Skyline file (she’ll come by between 12:30 and 2:30 pm)
  • Try BLAST on Hummingbird
  • Edit and publish Crab Meeting #6 DecaPod episode (at home in evening)


  • Work on R script for organizing new Qubit data
  • Come up with an extraction plan to finish by Dec 21st (when I leave for Holidays)
  • Determine how many kits need to order


  • Extract RNA using Qiagen RNeasy Micro Plus Kit from a subset of the samples I selected Wednesday
  • Check in on BLASTs
  • START WORKING ON GSS POSTER!!! GSS is Thurs Nov 15th

from Grace’s Lab Notebook