AutoQC- No existing files found

AutoQC- No existing files found davis  2019-09-20

Hi Skyline team!

I am a new user to AUTOQC. AutoQC is unable to import/find my existing files although the appropriate data folder is provided in the Folder to watch: field in the AutoQC Configuration settings. Please help me.

Current log message.

9/20/2019 8:25:27 AM] Getting the acquisition date on the newest file imported into the Skyline document.
[9/20/2019 8:25:27 AM] Running SkylineRunner.exe with args:
[9/20/2019 8:25:27 AM] --in="D:\Masslynx_projects\20180830_Metabolomics_Lipidomics.PRO\Skyline Results\AutoQC\" --report-conflict-resolution=overwrite --report-add="C:\Users\Administrator\AppData\Local\Apps\2.0\MY2EMOE9.LK6\QNADK77V.1XC\auto..tion_e4141a2a22107248_0001.0001_6f67fb96aa7015e7\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="D:\Masslynx_projects\20180830_Metabolomics_Lipidomics.PRO\Skyline Results\AutoQC\AcquisitionTimes.csv"
[9/20/2019 8:25:30 AM] The name 'AcquisitionTimes' already exists.
[9/20/2019 8:25:30 AM] Resolving conflicts by overwriting.
[9/20/2019 8:25:30 AM] Success! Imported Reports from FileAcquisitionTime
[9/20/2019 8:25:30 AM] Opening file...
[9/20/2019 8:25:30 AM] File opened.
[9/20/2019 8:25:30 AM] Exporting report AcquisitionTimes...
[9/20/2019 8:25:30 AM] Report AcquisitionTimes exported successfully to D:\Masslynx_projects\20180830_Metabolomics_Lipidomics.PRO\Skyline Results\AutoQC\AcquisitionTimes.csv.
[9/20/2019 8:25:30 AM] SkylineRunner.exe exited successfully.
[9/20/2019 8:25:30 AM] The most recent acquisition date in the Skyline document is 9/10/2018 5:46:08 AM
[9/20/2019 8:25:30 AM] Initializing Panorama pinger...
[9/20/2019 8:25:30 AM] Starting configuration...
[9/20/2019 8:25:30 AM] Importing existing files...
[9/20/2019 8:25:31 AM] No existing files found.

Best! Sonnet

Vagisha responded:  2019-09-20

Hi Sonnet,

I assume you have the correct instrument selected in your AutoQC Loader configuration. You have "Masslynx" in your file path so I am guessing that the data to be imported are in .raw directories. Can you please send me the AutoQC.log file for this configuration? You will find it in the same directory on your computer as your Skyline file.


davis responded:  2019-09-20

Hi Vigashi,

Thank you for your assistance. I have Waters selected in AutoQC Loader configuration. Please find the AutoQC.log file attached.

Best! S

Vagisha responded:  2019-09-22

Hi Sonnet,

I see the problem. You are using a "Contains" filter for the raw data you want to import, and you are giving comma-separated values as input to the filter:


Unfortunately, AutoQC Loader does not let you specify more than one string as input to the "Contains" filter so it is trying to find .raw directories that match the entire string above. You could try using the "Regular Expression" filter instead for this case. Something like this could work: