Hi,

I am following the tutorial on GitHub, but the Google Drive link to the demo dataset doesn't seem to work. https://github.com/SebVaca/Avant_garde/tree/master

Could you help check, and, if possible, attach a new link with your response? Thanks a lot!

Li

When I want to install avant-garde in Skyline I encounter this error: the remote severe returned an error: (400) bad request.
Can you please guide me on how can I solve the problem?
My Skyline version is: 21.2.0.425

Dear AvG support team,
I have been trying to run AvG version 0.0.1.5 in Skyline 21.1.0.146. ( PC: Intel(R) Core(TM) i5-9400 CPU @ 2.90 GHz, RAM: 16GB) for an analysis of 6 DIA raw files from a Q Exactive Plus. Prep_1 apparently works fine but in Prep_2 step (using From_current_Skyline_File or From_CSV_File) I got an error preventing me from proceeding with the analysis. I'd appreciate if you could help me to solve this issue.
Best regards,
Alejandro.

Dear AvG support 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 DIA-SWATH samples loaded and initially ran the Export Report -> AvantGardeDIA_Export. I made a 10GB MySQL database using the 'From_Current_Skyline_File' option. However, 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

Hi,

I've been wanting to run Avant-garde on a large DIA dataset. The tool works successfully for me on a smaller dataset however when the number of files increases, the step where a csv is exported from Skyline (only to then re-import it) is either taking a very long time, or just crashes. I've been hoping to find a way to run the tool circumventing the steps run in Skyline, but unfortunately have not been able to find sufficient information online to do so. I'd appreciate if I could help some help to get this started.

Best,
Franziska

Hello,

Currently I am trying to run AvG version 0.0.1.4 in Skyline Daily 20.1.1.83. Prep_1 and Prep_2 steps seem to work smoothly. However when I try to run any module in the Run_AvG_Module such as GlobalRefinement I get the error:

LaunchParallelTasks_ReadFromDB(ParamsFile,RefinementWorkflow)
Warning messages:
[1] "Parallel: Done!"
1: In connection_release(conn@ptr) :
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/tim_v/Downloads/ExampleAvG.sky/AvantGardeDIA/DataFormatting/TempFiles/Report_GR_ColNamesName_Tag.csv': No such file or directory
Execution halted

The full Skyline log is attached. I noticed that the script does not create the csv files as it should in *\DataFormatting\TempFiles. This obviously results in an error because it tries to open non-existing files.

I got the same error in Skyline Daily and the regular Skyline build.
The same error appeared on two different PC's.
The attached changelog is with R3.6.3 and the latest updates of the requirement packages.
The same error was returned when downgrading the packages to the minimal required versions as described in the AvG github page.
To minimize errors, I'm currently trying to run AvG on the demo set also provided in the AvG github page.

What could I try to fix the problem?

Any help is much appreciated!

Hi,

I'm posting regarding an issue with Avant-Garde for DIA using Skyline and am following the tutorial handed out at the 2019 Targeted Proteomics course in Barcelona. I believe I successfully went through all the described steps, but when I in the end pull up the Results Grid, the columns related to AvG (i.e. AvG_Score, Avg_SpectralLibSim_, etc.) do not appear. These columns are checked in the Document Settings>Annotations tab so I would expect that I can select them in the Results Grid or Document Grid, but this is not the case, even when opening the 'Customize View' option.

I'd appreciate if you could point me in the right direction in case this issue has come up in the past.
Thank you,
Franziska

Hi,
I am trying to install AvG and I already having R 3.6 installed on my computer. However, AvG always wants to install R-3.5.2. Is there a way to point it to the current R installation and only install the required packages?

Thanks,

Tomas

Hi, I get the following message whe trying to Create parameters file (TOF):

Installing Latest version of the AvantGardeDIA R package

install_Latest_AvG_RPackage<-file.path(args[5],"Update_AvG_RPackage.r")
source(install_Latest_AvG_RPackage)
Warning in install.packages(Avg_RPackage_path, repos = NULL) :
'lib = "C:/Program Files/R/R-3.5.2/library"' is not writable
Error in install.packages(Avg_RPackage_path, repos = NULL) :
unable to install packages
Calls: source -> withVisible -> eval -> eval -> install.packages
Execution halted

Dear all,

with the new skyline beta 19.0 but also with the normal skyline 4.2 I am not able to install and start AvG-DIA, which is something I would really like to do. It actully worked some time after release but when I now try to reinstall it something does not work (both skyline toolbox and zip import installation)

Could be an issue that the software does not have admin rights to write the needed R packages in the right directory under C:\Program Files\R\R-3.5.2

Could you please let me know if you have a workaround, or the info which files have to go where so that I can copy the packages manually to the correct destination.

Looking forward to get a short response.

Thank you for the tool and with best regards,
tobias

Hi,
so I just encountered a problem while trying to generate the SQLite DB for one of our datasets. I included the immediate window output. It looks like the tool expects more lines in the skyline output than there are. I tried running AvG with the demo set and another of our datasets and it worked just fine. I processed the data the same as always so I don't know what is causing this error. It would be great if you could have a look at it.
System info:
Windows 10, 64-Bit
i9-7960X @ 2.80Ghz
64 GB RAM
AvG version: 0.0.1.0
Skyline version: 4.2.0

If you need any additional info or the data itself please let me know.
Cheers,
Pascal