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Error in Panorama Upload Todd  2017-03-20
 
Hi,

We have been uploading DDA runs to Panorama (through AutoQC) for several months now without any major issues. We have used the latest Skyline-daily builds (currently 3.6.1.10556). Since about 3/9/2017, we have been getting errors at the end of the skyline file upload both when using AutoQC, or when trying to manually upload the files from within the Skyline application. I have attached the logs for the AutoQC (v1.1.0.10005) and the Skyline applications, and an example sky.zip file. We can't remember exactly whether this error coincided with our latest upgrade of Skyline-daily to the most recent build, but it might be related.

Thanks,
Todd
 
 
Todd responded:  2017-03-21
Hi,

I would like to provide an update to the issue described above. After restarting the computer a few times, AutoQC now uploads the sky.zip files without generating the above error message. I can verify that the latest sky.zip is an entry in the Runs tab of Panorama, but when trying to access the sky.zip file, there is no stored chromatogram or peak data. I opened the local skyline document and verified the 2 new data files were present and the chromatograms were extracted. Manually Publishing to Panorama is "successful", but the upload sky.zip again contains no chromatogram data according to Panorama. Let me know what data you would need, my sky.zip files are larger than 50MB so I have not included them as an attachment. Thanks in advance for any ideas why this might be happening.

Todd
 
vsharma responded:  2017-03-21
Hi Todd,

Can you please send me the URL of your Panorama folder so that I can take a look at the files?

Thanks,
Vagisha
 
Todd responded:  2017-03-21
 
vsharma responded:  2017-03-21
Hi Todd,

Skyline-daily 3.6.1.10556 (released March 1st) changed the format of the file that stores chromatogram data (.skyd file). Panorama does not understand this new format so ignores the chromatogram data. That is why you don't see any chromatograms in Panorama for files uploaded via AutoQC Loader. This should be fixed in the next release of Skyline-daily. Brendan is aware of this issue so I am sure that it will be fixed very soon.

Manual uploads from Skyline-daily (via "File" > "Publish to Panorama") should save the .skyd file in a version that Panorama understands. So, you should see chromatograms in Panorama for a manually uploaded file from Skyline-daily. However, since you are uploading this to a QC folder, and this same file (with the same set of replicates) was probably already uploaded via AutoQC Loader, Panorama thinks that there is no new QC data to import! I will be updating PanoramaWeb on Thursday which will change the way data is imported in QC folders -- data from the last uploaded Skyline document will overwrite older data. This update will at least help to get your chromatograms imported to Panorama via "File" > "Publish to Panorama" in Skyline.

The real fix to get your QC pipeline going again will have to be in Skyline-daily. I will get back to you as soon I have an estimate of when the next Skyline-daily will be released. I am really sorry about this.

Thanks,
Vagisha
 
Todd responded:  2017-03-21
Hi Vagisha,

Thank you for the detailed response, this makes sense. I agree, Skyline-daily updates usually roll out quickly, so we will wait for the next release.

-Todd