AvG global refinement: missing temporary file

support
AvG global refinement: missing temporary file willems533  2021-03-09
 

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 :

LaunchParallelTasks_ReadFromDB(ParamsFile,RefinementWorkflow)
Warning messages:
1: In connection_release(conn@ptr) :
[1] "Parallel: Done!"
Read_AndFormatResults()
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
Execution halted

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,
Patrick

 
 
Nick Shulman responded:  2021-03-09
If you want to create a CSV file which looks like what the external tool sees, you should go to:
File > Export > Report
and choose "Invariant" in the Language dropdown.

When you choose the "Invariant" language, the column headers will not have spaces in them, and all numbers will be formatted to show as many decimal places as the data has.

I don't know what could be causing the error that you are seeing. You should ask that question on the Avant Garde support page which is here:
https://skyline.ms/project/home/software/Skyline/tools/Support/AvantGardeDIA/begin.view?

-- Nick