Issue 801: BiblioSpec MaxQuant reader should look for all necessary raw data files and issue a block error about any that are missing

issues
Status:open
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:3
Milestone:21.2
Opened:2021-05-07 by Brendan MacLean
Changed:2021-05-07 by Brendan MacLean
Resolved:
Resolution:
Closed:
2021-05-07 Brendan MacLean
Title»BiblioSpec MaxQuant reader should look for all necessary raw data files and issue a block error about any that are missing
Assigned To»matt.chambers42@gmail.com
Type»Defect
Area»Skyline
Priority»3
Milestone»21.2
I have been working with a MaxQuant search of 47 DDA runs for which I also have the RAW data, but initially, the file names did not match what was listed in the msms.txt file. The first time BlibBuild appears to read the entire msms.txt file and then fail listing just one raw data file that it cannot find. I fixed that and then went through the long read of msms.txt again to be told the next raw data file had a similar issue. At this point, I realized that the files had _T0 appended to their basenames from what was listed in the msms.txt. So, I removed _T0 from all (I thought) of the file names, restarted the build and went to bed. In the morning, I found that I had missed one file, and so I had to restart the build again.

It would have been far better to have gotten a full list of all of the missing raw data files up front, which would have had the added benefit that by the time I went to bed I would have known for sure that BlibBuild felt it had all of the raw data files it needed.