Dear Skyline team,
I was recently trying to run the AvantGarde external tool (latest version 0.0.1.4) and ran into some errors.
I have nine samples loaded and initially ran the Export Report -> AvantGardeDIA_Export. However, when trying to create the MySQL database from this via 'From_CSV_file' it could not load in the CSV due to incorrect headers. Headers in the CSV were for instance 'Fragment Ion' while it was anticipating without a space I think 'FragmentIon'.
As the exported file was 27 GB omitting the spaces in the header was quite annoying. However, I managed to now generate the MySQL using the 'From_Current_Skyline_File' option that is normally recommended for smaller analysis. When now trying to run the GlobalRefinement option however it gives me :
1: In connection_release(conn@ptr) :
 "Parallel: Done!"
There are 1 result in use. The connection will be released when they are closed
2: In connection_release(conn@ptr) : Already disconnected
Error in file(file, "rt") : cannot open the connection
Calls: Read_AndFormatResults -> read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/pawil/Documents/Manuscripts/2021 - DIA2/DIA/MQ_lib/AvantGardeDIA/DataFormatting/TempFiles/Report_GR_ColNamesName_Tag.csv': No such file or directory
I noticed a very similar support topic here 'https://skyline.ms/announcements/home/support/thread.view?rowId=41003' where the solution was to have multiple files, which is already the case for my data.
Thanks in advance for your help,