PECAN Update 1
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:
- My raw files were not properly converted, and the data
pecanpieis looking for, the MS2 files, are not present.
- 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:
- Reconvert 1 raw file to an mzML format using the command line verson of MSConvert. The Evernote tutorial suggests this may be an issue.
- Concurrently, explore the .blib file that was generated by
pecanpiein Skyline. If this file has data, then everything should be fine!
Really hoping we fall into scenario 2 :pray:
Written on March 6, 2017