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Import of raw files and upload on Panorama with AutoQC

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Import of raw files and upload on Panorama with AutoQC pascaline bories  2025-05-02 12:29:04
 

Hi Panorama team,

I try to set up automatic import of files for QC with AutoQC.
I have several error messages in the log (attached) but I don't well understand why. It says that my Skyline file is in use but it is not. I checked for all the permissions to modify the file. Moreover, the Panorama upload works, but not all the time.

Also, when I add a file to the folder to watch, I see in the log that a file was added to directory but nothing happens.

Do not hesitate if you need more information.

Thank you in advance for your help,
Pascaline
 
 
Vagisha Sharma responded:  2025-05-05 00:12:19

Hi Pascaline,

Thanks for attaching the log file.

When you re-started the AutoQC Loader configuration on 2025-05-02 14:46:00, I see in the log that the document QC_20250424_CytoC_AST_Rapid150.sky was empty.

[2025-05-02 14:46:08] The Skyline document does not have any imported results.

The first import attempt was skipped because the replicate already existed in the document:

[2025-05-02 14:46:09] 202401004_AST-Rapid150_G05_CytoC_06.raw is ready
[2025-05-02 14:46:15] 202401004_AST-Rapid150_G05_CytoC_06 -> Z:\acquisitions\QC\CytoC\CytoC_AST_2025\202401004_AST-Rapid150_G05_CytoC_06.raw Note: The file has already been imported. Ignoring...

This is unexpected since there shouldn’t have been any replicates in the document at this point. Could you please confirm whether you started with an empty Skyline document?

Later, some raw files began importing, but failed with an error indicating that the file was in use by another process:

[2025-05-02 14:54:40] Adding results...
[2025-05-02 14:54:40] 1. Z:\acquisitions\QC\CytoC\CytoC_AST_2025\20250428_QC_AST_Rapid150_G5_CytoC_08.raw
[2025-05-02 14:54:40]
[2025-05-02 14:54:45] [1] 45%
[2025-05-02 14:54:47]
[2025-05-02 14:54:47] Updating peak statistics
[2025-05-02 14:54:47] ERROR: Error: Failure attempting to write the file Z:\resultats\QC\CytoC\CytoC_QC_AST\QC_20250424_CytoC_AST_Rapid150.skyd
[2025-05-02 14:54:47] Le processus ne peut pas acc‚der au fichier, car il est utilis‚ par un autre processus.

This makes me think that another instance of Skyline (or another AutoQC Loader configuration) may be importing raw data into the same document. Do you have multiple AutoQC Loader configurations running? If so, can you check that they are not using the same Skyline document?

Thanks,
Vagisha
 
pascaline bories responded:  2025-05-05 06:24:16

Hi Vagisha,

Thank you for your answer.

"This is unexpected since there shouldn’t have been any replicates in the document at this point. Could you please confirm whether you started with an empty Skyline document?"
In fact, I used the Skyline file for previous import, but as the new files in the folder were not imported, I removed all the results from the Skyline file in order to try to start again from zero..

"This makes me think that another instance of Skyline (or another AutoQC Loader configuration) may be importing raw data into the same document. Do you have multiple AutoQC Loader configurations running? If so, can you check that they are not using the same Skyline document?"
Yes other configurations were running but I created one Skyline file per configuration. I have this error message since the beginning I ran configurations. Even when I run only one AutoQC configuration. I checked the authorizations of editing the file. I thought it was enough to solve the issue but it was not.
As I have error messages from the beginning, I don't really understand.
Would you recommend to start again from scratch ? On another computer maybe ?

Thank you for your help !
Pascaline
 
Vagisha Sharma responded:  2025-05-05 09:56:10

Hi Pascaline,

This is odd! I think it would be easier to troubleshoot this over Zoom, where I can see your screen. I’ll reach out to you by email to schedule a time.

Thanks,
Vagisha