View Message
"unknown error connecting to the server" nod2007  2016-11-15
I started getting the message:

"unknown error connecting to the server"

about a week ago and have been unable to upload any results since. I haven't made any changes to the AUTOQC settings.
vsharma responded:  2016-11-15

Can you please tell me what version of AutoQC Loader and Skyline (or Skyline-daily) you are running? You can see the AutoQC Loader version in the title bar of the program window.

The AutoQC log (AutoQC.log) might have some more useful information. Can you send it to me, please? You will find it in the same folder as the Skyline document to which you are importing QC runs.

nod2007 responded:  2016-11-21

Thanks for responding.

We are running

Here is some info from a previously successful set from the log.
Below that are two different error examples.


Name: SC_RTC_test_102116
Enabled: True
Panorama User:
Created: 10/13/20166:38 PM
Modified: 10/21/201612:16 PM

Main Settings
Skyline file: C:\Users\Orbitrap Fusion\Documents\Skyline\
Folder to watch: D:\Bin\Stds\yWCE\2016
Include subfolders: False
Filter Type: Contains; Pattern: RTC
Instrument: Thermo
Results window: 120 days
Acquisition time: 85 minutes

Panorama Settings
Panorama server URL:
Panorama user email:
Panorama folder: /Weill%20Cornell%20MC%20-%20Dephoure%20Lab/SC_AUTOQC_101716

[10/25/2016 4:52:53 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[10/25/2016 4:52:53 PM] Running SkylineRunner.exe with args:
[10/25/2016 4:52:53 PM] --in="C:\Users\Orbitrap Fusion\Documents\Skyline\" --report-conflict-resolution=overwrite --report-add="C:\Users\Orbitrap Fusion\AppData\Local\Apps\2.0\X8DDRWOQ.604\8ERNVY82.0DJ\auto..tion_e4141a2a22107248_0001.0001_e2f4c913ae5d97ce\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Orbitrap Fusion\Documents\Skyline\AcquisitionTimes.csv"
[10/25/2016 4:52:54 PM] The name 'AcquisitionTimes' already exists.
[10/25/2016 4:52:54 PM] Resolving conflicts by overwriting.
[10/25/2016 4:52:54 PM] Success! Imported Reports from FileAcquisitionTime
[10/25/2016 4:52:54 PM] Opening file...
[10/25/2016 4:52:54 PM] File opened.
[10/25/2016 4:52:54 PM] Exporting report AcquisitionTimes...
[10/25/2016 4:52:54 PM] Report AcquisitionTimes exported successfully to C:\Users\Orbitrap Fusion\Documents\Skyline\AcquisitionTimes.csv.
[10/25/2016 4:52:54 PM] SkylineRunner.exe exited successfully.
[10/25/2016 4:52:54 PM] The most recent acquisition date in the Skyline document is 10/24/2016 11:24:12 AM
[10/25/2016 4:52:54 PM] Initializing Panorama pinger...
[10/25/2016 4:52:54 PM] Starting configuration...
[10/25/2016 4:52:54 PM] Importing existing files...
[10/25/2016 4:52:55 PM] Existing files found: 7
[10/25/2016 4:52:55 PM] yWCE_RTC_102116_f04904.raw was acquired (10/20/2016 10:09:55 PM) before the acquisition date (10/24/2016 11:24:12 AM) on the last imported file in the Skyline document. Skipping...
[10/25/2016 4:52:55 PM] yWCE_RTC_102216_f04918.raw was acquired (10/22/2016 12:10:38 AM) before the acquisition date (10/24/2016 11:24:12 AM) on the last imported file in the Skyline document. Skipping...
[10/25/2016 4:52:55 PM] yWCE_RTC_102216_f04924.raw was acquired (10/22/2016 8:30:15 AM) before the acquisition date (10/24/2016 11:24:12 AM) on the last imported file in the Skyline document. Skipping...
[10/25/2016 4:52:55 PM] yWCE_RTC_102316_f04940.raw was acquired (10/23/2016 5:43:01 AM) before the acquisition date (10/24/2016 11:24:12 AM) on the last imported file in the Skyline document. Skipping...
[10/25/2016 4:52:55 PM] yWCE_RTC_102316_f04943.raw was acquired (10/23/2016 9:08:34 PM) before the acquisition date (10/24/2016 11:24:12 AM) on the last imported file in the Skyline document. Skipping...
[10/25/2016 4:52:56 PM] yWCE_RTC_102416_f04955.raw is ready
[10/25/2016 4:52:56 PM] Running SkylineRunner.exe with args:
[10/25/2016 4:52:56 PM]
 --in="C:\Users\Orbitrap Fusion\Documents\Skyline\" --import-file="D:\Bin\Stds\yWCE\2016\yWCE_RTC_102416_f04955.raw" --import-on-or-after=10/24/2016 11:24:12 AM --save

[10/25/2016 4:52:56 PM] Opening file...
[10/25/2016 4:52:57 PM] File opened.
[10/25/2016 4:52:57 PM] Warning: The replicate yWCE_RTC_102416_f04955 already exists in the given document and the --import-append option is not specified. The replicate will not be added to the document.
[10/25/2016 4:52:57 PM] Saving file...
[10/25/2016 4:52:57 PM] File saved.
[10/25/2016 4:52:57 PM] SkylineRunner.exe exited successfully.
[10/25/2016 4:52:57 PM] yWCE_RTC_102516_f04967.raw is ready
[10/25/2016 4:52:57 PM] Running SkylineRunner.exe with args:
[10/25/2016 4:52:57 PM]
 --in="C:\Users\Orbitrap Fusion\Documents\Skyline\" --import-file="D:\Bin\Stds\yWCE\2016\yWCE_RTC_102516_f04967.raw" --import-on-or-after=10/24/2016 11:24:12 AM --save
 --panorama-server="" --panorama-folder="/Weill%20Cornell%20MC%20-%20Dephoure%20Lab/SC_AUTOQC_101716" --panorama-username=""
[10/25/2016 4:53:02 PM] Opening file...
[10/25/2016 4:53:02 PM] File opened.
[10/25/2016 4:53:02 PM] Adding results...
[10/25/2016 4:53:03 PM] Results added from yWCE_RTC_102516_f04967.raw to replicate yWCE_RTC_102516_f04967.
[10/25/2016 4:53:03 PM] Saving file...
[10/25/2016 4:53:03 PM] File saved.
[10/25/2016 4:53:05 PM] Uploaded 3.46 MB of 16.18 MB
[10/25/2016 4:53:05 PM] Successfully pinged Panorama server.
[10/25/2016 4:53:07 PM] 29% - Uploaded 9.48 MB of 16.18 MB
[10/25/2016 4:53:09 PM] 36% - Uploaded 11.95 MB of 16.18 MB
[10/25/2016 4:53:11 PM] 47% - Uploaded 15.41 MB of 16.18 MB
[10/25/2016 4:53:12 PM] 100% - Uploaded 16.18 MB of 16.18 MB
[10/25/2016 4:53:13 PM] Renaming temporary file on server
[10/25/2016 4:53:16 PM] Waiting for data import completion...
[10/25/2016 4:53:16 PM] SkylineRunner.exe exited successfully.
[10/25/2016 4:53:16 PM] Finished importing existing files...
[10/25/2016 4:53:16 PM] Importing new files...
[10/25/2016 4:53:16 PM] Waiting for files...
[10/25/2016 4:59:07 PM] Finished importing files.
[10/25/2016 4:59:45 PM] Initializing logging...
On November 7, we saw this:
[11/7/2016 8:27:41 AM] Waiting for files...
ERROR: Error pinging Panorama server
ERROR: The remote server returned an error: (401) Unauthorized.
   at System.Net.WebClient.UploadDataInternal(Uri address, String method, Byte[] data, WebRequest& request)
   at System.Net.WebClient.UploadString(Uri address, String method, String data)
   at AutoQC.WebPanoramaClient.PingPanorama(String folderPath, String username, String password)
   at AutoQC.PanoramaPinger.PingPanoramaServer()
Since then, we only get something like the following every time.

[11/9/2016 11:26:44 AM] f05106.raw is ready
[11/9/2016 11:26:44 AM] Running SkylineRunner.exe with args:
[11/9/2016 11:26:44 AM]
 --in="C:\Users\Orbitrap Fusion\Documents\Skyline\" --import-file="D:\Bin\Stds\yWCE\2016\wRTC\f05106.raw" --import-on-or-after=11/6/2016 2:44:14 PM --save
 --panorama-server="" --panorama-folder="/Weill%20Cornell%20MC%20-%20Dephoure%20Lab/SC_AUTOQC_101716" --panorama-username=""
[11/9/2016 11:26:48 AM] Unknown error connecting to the server
[11/9/2016 11:26:48 AM] Exiting...
[11/9/2016 11:26:48 AM] SkylineRunner.exe exited successfully.
[11/9/2016 11:26:48 AM] Finished importing existing files...
[11/9/2016 11:26:48 AM] Importing new files...
nod2007 responded:  2016-11-21
Here's the full log file.
vsharma responded:  2016-11-22
Hi Noah,

Thanks for sharing the log file. Unfortunately there is no additional information in the log file that will help me diagnose this problem. Could you please try a couple of things:

1. On your instrument computer upload a document to Panorama directly from Skyline ("Publish to Panorama" button in the toolbar OR File > Publish to Panorama)

This will likely fail too, but let me know if it succeeds.

2. If 1) fails, try to install an external tool in Skyline from the tool store: Tools > Tool Store...

If 2) fails with this error message: "Error connecting to the Tool Store: The request was aborted: Could not create SSL/TLS secure channel." it means that your operating system does not support the protocol Skyline is using for SSL connections. In this case you will have to go through Windows updates. See this support board request on the Skyline website:
You may be able to get a stand-alone package for the update here:

If 1) and / or 2) are successful we may have to do a WebEx call to try to debug this.