Laura’s Notebook: Pecan Again?!

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

2017-03-13_adding-prtc-to-stress-proteome

Use Protein Digestion Simulator to execute in silico digestion

2017-03-13_digest-settings1

2017-03-13_digest-settings2

2017-03-13_digest-settings3

2017-03-13_digest-settings4

2017-03-13_digest-complete

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

2017-02-19_galaxy-uploading-digested

2017-02-19_galaxy-digested-unedited

2017-02-19_galaxy-cut-column

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

2017-02-19_galaxy-trimmed-header

Killing existing Pecan run

2017-03-13_killing-pecan

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

2017-03-13_pecan-input-files

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

2017-03-13_running-pecan6

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

2017-03-13_pecan6-queue

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

2017-03-13_making-jobs-executable

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

from The Shell Game http://ift.tt/2ny4Y7j
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