Hit an obstacle with PECAN this weekend.

On Saturday, I used ssh to examine pecanpie progress on Roadrunner. I saw this…

…and thought I was done!

However, Sean checked the PECAN log file and saw that there were no MS2 files scanned. Lots of discussion on Github ensued. There are a few possibilities:

1. My raw files were not properly converted, and the data pecanpie is looking for, the MS2 files, are not present.
2. Everything worked out fine, and this is just an artifact of the analyses!

Interestingly enough, using pecanpie already requires the use of a typo for the isolation scheme (specifying “BOARDER” instead of the correctly spelled “BORDER”). Maybe our paucity of PECAN understanding is making this all seem more complicated then it is! I talked to Sam and came up wtih a game plan going forward:

1. Reconvert 1 raw file to an mzML format using the command line verson of MSConvert. The Evernote tutorial suggests this may be an issue.
2. Concurrently, explore the .blib file that was generated by pecanpie in Skyline. If this file has data, then everything should be fine!

Really hoping we fall into scenario 2 :pray: