Results not being pushed to Panorama

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Results not being pushed to Panorama pnlabsg  2017-09-20
 
Dear Panorama developers,

We have been using autoQC for just over a month, and found that our QC results not being pushed to Panorama for the past few days. I suspect a conflict in Skyline having to add a new file and remove a old file at the same time (a typical log with this problem is shown below).

We can get around this by removing the latest file in the Skyline document, then restarting autoQC again. Our AutoQC version is 1.1.0.11134, and Skyline version is 3.7.0.11317 64 bit.

Please advise on how to get automatic uploading working again.

Best regards,
Liyan

[20-Sep-17 10:09:17 PM] Waiting for files...
[21-Sep-17 11:13:39 AM] 20170921_RS_BSA_PRM_1.raw added to directory.
[21-Sep-17 11:13:39 AM] 20170921_RS_BSA_PRM_1.raw is being acquired. Waiting...
[21-Sep-17 11:53:39 AM] 20170921_RS_BSA_PRM_1.raw is ready
[21-Sep-17 11:53:39 AM] Running SkylineRunner.exe with args:
[21-Sep-17 11:53:39 AM]
 --in="D:\Skyline autoQC\HF_BSA_autoQC_refined.sky" --remove-before=22-Aug-17 --import-file="D:\MS_DATA_HF\20170921_RS_BSA_PRM_1.raw" --import-on-or-after=22-Aug-17 --save
 --panorama-server="https://panoramaweb.org/" --panorama-folder="Nanyang Tech U – PN Lab/QC/HF" --panorama-username="pnlabsg@gmail.com"
[21-Sep-17 11:53:43 AM] Opening file...
[21-Sep-17 11:53:44 AM] File HF_BSA_autoQC_refined.sky opened.
[21-Sep-17 11:53:44 AM]
[21-Sep-17 11:53:44 AM] Adding results...
[21-Sep-17 11:53:44 AM] 1. D:\MS_DATA_HF\20170921_RS_BSA_PRM_1.raw
[21-Sep-17 11:53:44 AM]
[21-Sep-17 11:53:48 AM] [1] 29%
[21-Sep-17 11:53:50 AM] [1] 45%
[21-Sep-17 11:53:52 AM] [1] 56%
[21-Sep-17 11:53:54 AM] [1] 64%
[21-Sep-17 11:53:57 AM]
[21-Sep-17 11:53:57 AM] Updating peak statistics
[21-Sep-17 11:53:57 AM] Joining file D:\Skyline autoQC\20170921_RS_BSA_PRM_1_453968865.raw.skyd
[21-Sep-17 11:53:57 AM] Removing results before 22-Aug-17...
[21-Sep-17 11:53:57 AM] Removed D:\MS_DATA_HF\20170821_RS_BSA_PRM_1.raw.
[21-Sep-17 11:53:57 AM] Saving file...
[21-Sep-17 11:53:57 AM] File HF_BSA_autoQC_refined.sky saved.
[21-Sep-17 12:01:23 PM] SkylineRunner.exe exited successfully.
[21-Sep-17 12:01:23 PM] Waiting for files...
 
 
vsharma responded:  2017-09-21
Hi Liyan,

Thank you for your question. I looked at your QC folder on PanoramaWeb (https://panoramaweb.org/labkey/project/Nanyang%20Tech%20U%20%E2%80%93%20PN%20Lab/QC/HF/begin.view?) and it does look like the Skyline document with the raw file 20170921_RS_BSA_PRM_1.raw got uploaded and imported (see attached screenshot). Was this uploaded after you removed the raw file from the Skyline document and re-started AutoQC Loader?

Can you please send me the complete AutoQC.log file?

Thanks,
Vagisha
 
pnlabsg responded:  2017-09-21
Dear Vagisha,

Yes, the file was only uploaded after I removed it from Skyline and re-started autoQC.

Please find attached the full log.
 
vsharma responded:  2017-09-22
Hi Liyan,

Thank you for sending me the log file. I think you might be right - I can see at least 3 instances of Panorama upload not happening when a raw file is also removed from the Skyline document. This is unexpected behavior. The correct command is being issued to SkylineRunner (AutoQC calls Skyline, via Skylinerunner, to do the raw file import, and upload to Panorama). I just looked at the code and can't see any obvious bugs. Can you please upload your raw file (D:\MS_DATA_HF\20170921_RS_BSA_PRM_1.raw) to this location on PanoramaWeb:

https://panoramaweb.org/labkey/project/00Developer/vsharma/Issues/Results_not_uploaded_to_panorama_liyan/begin.view

I have given your account (pnlabsg@gmail.com) permission to upload in this folder. There is an "Upload files" button in the "Files" box. Let me know if you are not able to upload.

Thanks a lot for reporting the bug and for your help in figuring it out.

-Vagisha
 
pnlabsg responded:  2017-09-25
Dear Vagisha,

Thanks for your reply. I have uploaded the file to the location specified.

Additionally, this may relate to why there's a problem for us: occasionally, Skyline would encounter an error (Windows-related?) that seems to cause it to crash. This is without Skyline being opened and it happens on both data acquisition PCs running AutoQC. The error prompt is shown below:

Problem signature:
  Problem Event Name:    CLR20r3
  Problem Signature 01:    Skyline.exe
  Problem Signature 02:    1.0.0.0
  Problem Signature 03:    59b4a48d
  Problem Signature 04:    Skyline
  Problem Signature 05:    1.0.0.0
  Problem Signature 06:    59b4a48d
  Problem Signature 07:    773e
  Problem Signature 08:    24
  Problem Signature 09:    pwiz.Skyline.Util.Assumption
  OS Version:    6.1.7601.2.1.0.256.48
  Locale ID:    1033
  Additional Information 1:    a009
  Additional Information 2:    a009ab7e5257d08d5d1625b49477e8fe
  Additional Information 3:    f7c4
  Additional Information 4:    f7c4e930a901e4d255f6d5d1eb659931

It doesn't seem to cause any noticeable issue other than forcing us to acknowledge the error, but may be related to this issue.
 
vsharma responded:  2017-09-26
Hi Liyan,

I've identified the bug that is causing this problem. And, yes, the Skyline error you are seeing is related to this issue.

This will be fixed in the next Skyline-daily release. But I don't know if a patch release is planned anytime soon for the public release of Skyline 3.7 (what you are using). I will check with Brendan and let you know if he has any plans to put out a patch release.

In the mean time, when you see the problem again, just let AutoQC Loader keep running since the raw file gets imported into the Skyline document. The error only happens just before the attempt to upload to Panorama. When the next raw file gets imported and no replicate is removed, the document will be uploaded to Panorama and it will include results from the previous raw file. You won't see your results immediately but at least you will not have to stop/start AutoQC Loader.

Another option, if you want to see your results right after they get imported, is to upload the document to Panorama yourself by opening it in Skyline and uploading it to Panorama through the File > Publish to Panorama menu. Be sure to close the document after this as AutoQC Loader is not able to import raw files to a document that is open in Skyline.

These are not ideal workarounds. Sorry! I will get back to you if there is a patch release of Skyline 3.7 planned anytime soon.

Thanks,
Vagisha
 
pnlabsg responded:  2017-09-26
Hi Vagisha,

Thanks for the reply, glad to see the bug is identified. We will make do with the workaround for now since sometimes we will want to monitor instrument performance after calibration. Hopefully this will get resolved!