Yep.

Steven prepared a smaller geoduck proteome for me, edited to only include proteins related to stress response. This decreased the # proteins from ~30,000 to 600, the idea being that Pecan will run faster and won’t max out its “temporary memory.” Here’s the synopsis of me preparing files and running Pecan:

Add PRTC sequence to the new database

Use Protein Digestion Simulator to execute in silico digestion

Use Galaxy online to remove excess columns; note that the output from PDS is a .txt file

Resulting edited file (note this is a .tabular format, which is fine)

Killing existing Pecan run

Copied input files into new folder entitled “Pecan-inputs6” - This is the 6th Pecan run attempted on this data.

Executing Pecan; note that I needed to edit the file paths (output and input)

Checking to see that there is, in fact, a Pecan job queue

Making the .job files in /percolator/ and /pecan2blib/ directories executable

This “Pecan6” run was started at ~3:30pm - I’m curious to see how quickly things go with this reduced background proteome!