Demultiplexing Update 2

Another new MSConvert CLI

Over the weekend, I was only able to convert 2 oyster .raw file, which can be found in this OWL folder. Austin figured out that another program, Prism, slows down after a given number of isolation windows. He rewrote our msconvert CLI, and Emma brought it over this morning.

Before we tried the new version, I shared the converted oyster1.mzML file with her so she can test it on pecanpie. Her notebook has the information for our test, which can be found here.

First, I unzipped the new version of msconvert under srlab » Documents » oystertest » oystertest2. I also made a copy of the config file and pasted it into oystertest2 (filename: config_fix.txt). I then ran the following code to convert oyster1.raw using the updated program.

cd C:\Users\srlab\Documents\oystertest\oystertest2

msconvert.exe -c config_fix.txt 2017_January_23_envtstress_oyster1.raw


Within minutes, the file finished converting! I uploaded to this OWL link.

I moved oyster1.raw to the folder oystertest » finished-raw. I then started converting the rest of my oyster .raw files.

msconvert.exe -c config_fix.txt *.raw


I’m going to check on the files over the course of the day, and will upload them to this OWL folder.

Written on April 17, 2017