Showing: limited to 100 messages
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Problems uploading files and them being recognized |
(1 response) |
mmart137 |
2021-03-15 16:43:51 |
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Hi, I'm trying to publish a full dataset for a paper. When I hit submit, it says that there are files missing that have clearly been uploaded. In addition, it is asking for new, different raw files that it says are missing every time I hit 'resubmit'. Can you please help here? Thanks! Best, Marissa
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view message |
Problem uploading Skyline file to home folder |
(1 response) |
michael-e-wright |
2021-03-02 10:21:47 |
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Can't access home folder to upload a Skyline file. Am I doing something wrong? Also, how do I control permissions to view the folder?
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ErrorUploadtoPanaroma.png |
view message |
Problems with AutoQC loader |
(5 responses) |
a gorol |
2021-01-05 01:35:08 |
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Hello,
since yesterday i have problems with uploading QC Files to Panorama. We are using the AutoQC loader since May last year and it worked perfectly for us. Since yesterday i can not start the configuration anymore. The log File gives me several error messages but i don`t know how to solve this issue. I attached the LogFiles. I assume there is a problem with the skyline document but since this is the same one we are using since May I am not sure. Can you help us?
Best,
Alex
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AutoQC.log |
view message |
Uploading error to Panorama |
(2 responses) |
roberthardt |
2021-01-04 06:16:41 |
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Dear Skyline-Team,
I cannot upload any sky-zip files to the Panorama server anymore. I'm pretty confident that this has been caused by myself while using the "Cancel upload" button within Skyline daily. I also tried by myself cleaning the upload queue within Panorama, but this is also not working. I guess the server itself somehow got stuck?
Best
Robert
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panorama canceling.PNG panorama canceling2.PNG |
view message |
Error while uploading data to Panorama from Skyline-daily |
(1 response) |
hana kucharikova |
2020-11-06 06:58:32 |
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Hello,
I have encountered an error while uploading data from Skyline-daily (20.1.1.299) to Panorama. I am using GoogleChrome web-browser and Windows 10 OS (OS build 18363.1139).
I have opened my Skyline document, in section File press Upoload to Panorama, selected folder and start uploading the file. At the end of upload (when 98% was finished) an error message appear.
"Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02];"
There was also warning about Skyline versions incompatibility: "The version of this Skyline document is 20.14. This is newer than the highest supported version 4.1".
I have tried the upload again into new folder and after the notes in Skyline were removed, neither helped.
Detail information about the error log are in the attachment.
Can you, please, help me? Thank you, Hana
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Panorama upload_log_error |
view message |
AutoQC loader disconnects from local servers |
(2 responses) |
David Kotol |
2020-10-20 05:14:53 |
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Hi,
I have been struggling with the AutoQC for some time now. It works great but just for about 24 hours. Then I lose connection to local server where the data, in this case Thermo raw files, is stored. The connection to server remains lost until the PC is restarted.
To describe the problem:
1. QC sample is measured
2. Resulting file is automatically pushed to MassStorage local server (using
scheduler and .bat script) and to a designated folder
3. Another computer is running the AutoQC Loader and is paired
with the designated folder on the server
4. The QC software locates the result file on the server and uploads it
to the Panorama
This works for about 24 hours and then connection to the server is lost. The connection is restored by restarting the computer. But just for another 24 hours or so.
What I tried with always the same result:
- reinstall AutoQC Loader
- update AutoQC Loader
- use different computer
- reinstall and update Skyline
Is this a known issue or is it something with the servers of my institution, please? The institutional IT guys claim it is the software so I just want to check if anyone experienced this issue when loading raw files from servers and not the local storage.
All the best,
David
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view message |
AutoQC and skyline stuck at IMPORT WAITING |
(2 responses) |
DennisGoldfarb |
2020-10-06 06:51:13 |
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I created a new AutoQC folder, but am having trouble uploading to it. I tried cancelling everything in the data pipeline, but those are now stuck in "cancelling". Any help would be appreciated. Thanks.
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view message |
Unable to authenticate my panorama site password and email within Auto QC |
(2 responses) |
chris brown-2 |
2020-09-29 14:01:19 |
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Hello - I am unable to sign in to my panorama account and password in AutoQC to upload QC data.
Skyline account: 20.1.0.31 AutoQC loader 1.1.0.20237
Location of Panorama Folder: /Corteva Agrisciences - MSCOE/Lumos-Daily QC
Exact error message: Configuration Validation Error The username and password could not be authenticated with the panorama server.
Let me know what else you need.
Thanks, cjb
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view message |
Panorama for AutoQC |
(1 response) |
imene bousahba |
2020-09-17 03:23:10 |
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Hello, I wanted to know if it is necessary to use panorama for AutoQC (to publish my files in purpose to view the results) If not how can i do ? Thank you very much
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view message |
New Auto-QC install and transferring Configurations |
(1 response) |
Alejandro Cohen |
2020-09-01 10:19:07 |
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Hi!!
I'm transferring my configurations from one computer to another in a new installation of AutoQC (1.1.0.20237). I followed the instructions as per your email and get the error attached. The passwords are there in the original configurations. I tried editing the .xml file with the correct password, but that does not seem to work either
Is there a way around this?
Thanks
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Trouble Shoot Auto QC_Screen shots.docx |
view message |
Error uploading from skyline-daily but not skyline |
(2 responses) |
d foschepoth |
2020-08-06 11:47:01 |
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Hi,
I want to upload a bunch of skyline files and all but two of them I could readily upload using Skyline 20.1.0.155 without issues. But two files provided by a colleague were opviously edited with a newer version so I used skyline-daily to upload. Upon Üpload to Panorama" I get this error message of a connection error (The program added some german text in the error report):
Brief german list of ingredients:
Zeile = Line
bei =at
Ende der internen Ausnahmestapelüberwachung = End of internal exception stack monitoring (or so)
---------------------------
System.Reflection.TargetInvocationException: Failed attempting to retrieve information from the following servers:
https://panoramaweb.org/ ---> System.Exception: Failed attempting to retrieve information from the following servers:
https://panoramaweb.org/
bei pwiz.Skyline.FileUI.PublishDocumentDlg.PublishDocumentDlgLoad(List`1 listServerFolders) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PublishDocumentDlg.cs:Zeile 139.
bei pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:Zeile 254.
--- Ende der internen Ausnahmestapelüberwachung ---
bei pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:Zeile 1942.
bei pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:Zeile 202.
bei pwiz.Skyline.FileUI.PublishDocumentDlg.PublishDocumentDlg_Load(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PublishDocumentDlg.cs:Zeile 88.
------------------------------
I tried with the most recent versions of skyline-daily on multiple computers. Always same outcome. The current version is 20.1.1.213 of skyline-daily.
Any ideas what could be the cause for this?
Thanks in advance
David
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view message |
Manuscript on Biotin Acceptor Peptide |
(3 responses) |
akulyyasov |
2020-08-06 05:40:33 |
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Dear Skyline/Panorama team and users, I have uploaded the graphical abstract of the manuscript which I prepared during lockdown time. In this paper, I summarized the application of Biotin Acceptor Peptide 1070 which is used in proximity utilizing biotinylation method. The paper contains the description of its design, construction, and quantitation by Skyline software on the example of DNA dependent interaction of Sox2 and Oct4. If someone would like to read the text of the article, please send a message to my address kulyyasov@biocenter.kz
I will be very grateful for any help in improving the text, remarks, and comments on this manuscript.
With best regards, Arman
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JP_BAP_graphical_abstract.png |
view message |
Creating folders |
(1 response) |
weixiandeng1990 |
2020-07-24 18:39:07 |
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I can't see creating folder tab on the dashboard where it is supposed to be. Is it because I'm not an administrator of the lab account?
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view message |
AutoQC problem |
(1 response) |
eversa |
2020-07-23 13:11:49 |
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Hi, I tried to run a AutoQC and got the below error message:
--in="C:\ZWC-autoQC\test.sky" --remove-before=6/23/2020 --import-file="C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw" --import-on-or-after=6/23/2020 --save --panorama-server="https://panoramaweb.org/" --panorama-folder="Washington University STL - Evers Lab/AutoQC" --panorama-username="eversa@wustl.edu" [7/23/2020 2:26:58 PM] Opening file... [7/23/2020 2:26:59 PM] File test.sky opened. [7/23/2020 2:27:00 PM] [7/23/2020 2:27:00 PM] Adding results... [7/23/2020 2:27:00 PM] 1. C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw [7/23/2020 2:27:00 PM] [7/23/2020 2:27:01 PM] ERROR: Error: Failed importing the results file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw. [7/23/2020 2:27:01 PM] Message: pwiz.Skyline.Model.Results.MissingDataException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used. ---> pwiz.Skyline.Model.Results.NoFullScanFilteringException: The file C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used. [7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.SpectraChromDataProvider..ctor(MsDataFileImpl dataFile, ChromFileInfo fileInfo, SrmDocument document, IRetentionTimePredictor retentionTimePredictor, String cachePath, IProgressStatus status, Int32 startPercent, Int32 endPercent, IProgressMonitor loader) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 98 [7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.CreateSpectraChromProvider(MsDataFileImpl dataFile, ChromFileInfo fileInfo) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1265 [7/23/2020 2:27:01 PM] at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 237 [7/23/2020 2:27:01 PM] --- End of inner exception stack trace --- [7/23/2020 2:27:01 PM] [7/23/2020 2:27:01 PM] ERROR: SkylineRunner.exe exited with code 0. Skyline document import failed. [7/23/2020 2:27:01 PM] Adding C:\ZWC-autoQC\ZWC_459_a1b3_10uMOPD.raw to the re-import queue. [7/23/2020 2:27:01 PM] Attempting to re-import C:\ZWC-autoQC\ZWC_459_a1b3_30uMOPD_200719145246.raw. [7/23/2020 2:27:01 PM] ZWC_459_a1b3_30uMOPD_200719145246.raw is ready [7/23/2020 2:27:01 PM] Running SkylineRunner.exe with args: [7/23/2020 2:27:01 PM]
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view message |
Insufficient system resources |
(18 responses) |
Tobias Kockmann |
2020-07-23 02:24:44 |
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Hi Panorama support,
I am getting the following error message when trying to execute autoQC:
PLATFORM VERSION INFO
Windows : 6.3.9600.0 (Win32NT)
Common Language Runtime : 4.0.30319.42000
System.Deployment.dll : 4.7.3062.0 built by: NET472REL1
clr.dll : 4.7.3221.0 built by: NET472REL1LAST_C
dfdll.dll : 4.7.3062.0 built by: NET472REL1
dfshim.dll : 6.3.9600.16384 (winblue_rtm.130821-1623)
SOURCES
Deployment url : file:///C:/Users/autoQC_user/AppData/Roaming/Microsoft/Windows/Start%20Menu/Programs/AutoQC/AutoQC.appref-ms%7C
Deployment Provider url : http://skyline.gs.washington.edu/software/AutoQC/AutoQC.application
ERROR SUMMARY
Below is a summary of the errors, details of these errors are listed later in the log.
* Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\AutoQC\AutoQC.appref-ms| resulted in exception. Following failure messages were detected:
+ Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
COMPONENT STORE TRANSACTION FAILURE SUMMARY
No transaction error was detected.
WARNINGS
There were no warnings during this operation.
OPERATION PROGRESS STATUS
* [7/23/2020 11:07:47 AM] : Activation of C:\Users\autoQC_user\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\AutoQC\AutoQC.appref-ms| has started.
* [7/23/2020 11:07:47 AM] : Performing necessary update check as specified by the deployment.
ERROR DETAILS
Following errors were detected during this operation.
* [7/23/2020 11:07:49 AM] System.Runtime.InteropServices.COMException
- Insufficient system resources exist to complete the requested service. (Exception from HRESULT: 0x800705AA)
- Source: mscorlib
- Stack trace:
at System.Deployment.Internal.Isolation.IsolationInterop.CreateActContext(CreateActContextParameters& Params)
at System.Deployment.Internal.Isolation.IsolationInterop.CreateActContext(IDefinitionAppId AppId)
at System.ActivationContext.CreateFromName(ApplicationIdentity applicationIdentity)
at System.Deployment.Application.ApplicationActivator.Activate(DefinitionAppId appId, AssemblyManifest appManifest, String activationParameter, Boolean useActivationParameter)
at System.Deployment.Application.ApplicationActivator.ProcessOrFollowShortcut(String shortcutFile, String& errorPageUrl, TempFile& deployFile)
at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl, Uri& deploymentUri)
at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivationWithRetry(Uri activationUri, Boolean isShortcut, String textualSubId, String deploymentProviderUrlFromExtension, BrowserSettings browserSettings, String& errorPageUrl)
at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
COMPONENT STORE TRANSACTION DETAILS
No transaction information is available.
Any idea what this might indicate?
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view message |
DIA can't demultiplex |
(1 response) |
wendy white |
2020-06-18 11:35:55 |
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I made a DIA overlap method on the instrument- but when I use MS Convert GUI, it fails and reports this error:
------------------------------
Starting...
Opening file "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.raw" for read...
Calculating SHA1 checksum...
Processing...
Writing "C:\Users\WHITEW01\Desktop\Histones\2020_0617_histones.mzML"...
Failed - System.Exception: SpectrumToIndices() Number of demultiplexing windows changed. Minimum window size or window boundary tolerance may be set too low.
at pwiz.CLI.msdata.MSDataFile.write(MSData msd, String filename, WriteConfig config, IterationListenerRegistry iterationListenerRegistry)
at MSConvertGUI.MainLogic.processFile(String filename, Config config, ReaderList readers, Map`2 usedOutputFilenames)
at MSConvertGUI.MainLogic.Go(Config config, Map`2 usedOutputFilenames).
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view message |
Building Overlap DIA on Thermo Exploris 480 |
(1 response) |
wendy white |
2020-06-18 11:34:50 |
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I want to quantitate histone modifications using Thermo Exploris 480. When I make the acquisition method from Skyline, this error is displayed: Columns don’t match:
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error DIA exploris.docx |
view message |
Problems adding new chromatograms to assay library |
(4 responses) |
Andreas Hober |
2020-05-08 06:28:13 |
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Hi, I have a Panorama Assay Library to which I have uploaded several runs from one of our mass spectrometers. However, recently we have had some problems while rerunning some samples. Since the proteins already exist in the library we get prompted with the following message: "There are 36 conflicting proteins in this folder. Resolve conflicts", but when we try to update these proteins an error occurs (see attached screenshot).
How can we resolve this issue?
Best regards, Andreas
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Screen Shot 2020-05-08 at 15.23.03.png |
view message |
Recurring Error pinging Panorama server |
(7 responses) |
Roman Sakson |
2020-05-04 01:04:52 |
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Dear Panorama Team,
we seem to have recurring troubles pinging the Panorama server (it started already before Easter and goes on). Remarkably, it seems to work every now and then, so that we can upload our QC files, however, delays do occur and I would like to understand where this error comes from (to my knowledge, we did not change anything regarding our internet connection). A typical error message looks like this (could go on for hours or even days):
[5/4/2020 5:20:42 AM] ERROR: [5/4/2020 5:20:42 AM] Error pinging Panorama server https://panoramaweb.org/
System.Net.WebException: Unable to connect to the remote server ---> System.Net.Sockets.SocketException: A connection attempt failed because the connected party did not properly respond after a period of time, or established connection failed because connected host has failed to respond 128.95.55.201:443 at System.Net.Sockets.Socket.DoConnect(EndPoint endPointSnapshot, SocketAddress socketAddress) at System.Net.ServicePoint.ConnectSocketInternal(Boolean connectFailure, Socket s4, Socket s6, Socket& socket, IPAddress& address, ConnectSocketState state, IAsyncResult asyncResult, Exception& exception) --- End of inner exception stack trace --- at System.Net.WebClient.UploadValues(Uri address, String method, NameValueCollection data) at AutoQC.WebClientWithCredentials.Post(Uri uri, NameValueCollection postData) at AutoQC.WebPanoramaClient.PingPanorama(String folderPath, String username, String password) at AutoQC.PanoramaPinger.PingPanoramaServer()
Thank you very much in advance!
Roman
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view message |
ERROR: Index 0 out of bounds for length 0 |
(3 responses) |
Maithreyan |
2020-04-27 08:21:41 |
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When I try to upload the QC data from Skyline to panorama, I am getting the following error, I have attached the log file. I think it is something to do with our data. Could you please explain it. Also, Auto QC is not uploading the data automatically to Panorama even after giving the required details for panorama.
27 Apr 2020 08:12:43,074 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' 27 Apr 2020 08:12:43,079 ERROR: Index 0 out of bounds for length 0 java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
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QC_2020-04-27_17-10-51.sky_2020-04-27_08-12-17.log |
view message |
Error when resubmitting data |
(1 response) |
Markus |
2020-04-25 14:21:31 |
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Dear Panoramaweb team,
during revision we have added a second dataset to a project, which had already received a ProteomeXchange ID for review before. I have now added all data to the existing project and then tried to resubmit but I get the following error: You are not authorized to edit the short URL 'fK1Nbw'
The former submission was done by a colleague of mine (who has meanwhile left) but I have full rights for the project - could that still be the problem?
Many thanks in advance for your help with this! BTW, would the PX-ID remain the same or would a new one be assigned?
Cheers, Markus
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view message |
Upload to Panorama error - ERROR: MoleculeId: Value is too long for column 'MoleculeId' |
(1 response) |
emmanuel varesio |
2020-04-23 10:06:31 |
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Hi,
I'm setting up two similar autoQC configurations for either ACN or MeOH gradient SST with the same LCMS QC mix for a Waters H-Class - G2 TOF MS.
Raw data filenames are similar, folder names for each solvent are similar, the two Skyline template files have the same molecule names and transitions for MH+ .... in brief everything is the same except that it's either ACN or MeOH written in the names.
When running the MeOH AutoQC loader config this works fine, but when switching to ACN dataset I got the following error message at the stage when the Skyline zip file is apparently uploaded to Panorama server.
Any help appreciated.
Best,
Emmanuel
23 Apr 2020 09:53:26,365 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority' 23 Apr 2020 09:53:26,392 INFO : Starting to import Skyline document from QC_Xevo-ACN_LCMS_QCmix_PrecOnly_2020-04-23_18-52-59.sky.zip 23 Apr 2020 09:53:26,395 INFO : Expanding QC_Xevo-ACN_LCMS_QCmix_PrecOnly.skyd 23 Apr 2020 09:53:26,451 INFO : Expanding QC_Xevo-ACN_LCMS_QCmix_PrecOnly.sky.view 23 Apr 2020 09:53:26,464 INFO : Expanding QC_Xevo-ACN_LCMS_QCmix_PrecOnly.sky 23 Apr 2020 09:53:26,476 WARN : The version of this Skyline document is 20.11. This is newer than the highest supported version 4.1 23 Apr 2020 09:53:26,486 INFO : 8% Done 23 Apr 2020 09:53:26,851 INFO : 11% Done 23 Apr 2020 09:53:26,852 INFO : Inserting QC-Xevo_LC_ACN 23 Apr 2020 09:53:26,865 INFO : 16% Done 23 Apr 2020 09:53:26,895 INFO : 19% Done 23 Apr 2020 09:53:26,918 INFO : 27% Done 23 Apr 2020 09:53:26,939 INFO : 31% Done 23 Apr 2020 09:53:26,978 INFO : 39% Done 23 Apr 2020 09:53:27,001 INFO : 43% Done 23 Apr 2020 09:53:27,021 INFO : 50% Done 23 Apr 2020 09:53:27,102 INFO : 55% Done 23 Apr 2020 09:53:27,630 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' 23 Apr 2020 09:53:27,633 ERROR: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long. Caused by: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long. 23 Apr 2020 09:53:27,729 ERROR: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long. org.labkey.api.query.RuntimeValidationException: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long. Caused by: MoleculeId: Value is too long for column 'MoleculeId', a maximum length of 200 is allowed. Supplied value was 241 characters long.
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view message |
Auto QC Trend report |
(4 responses) |
Srujana |
2020-04-16 13:11:03 |
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Hi,
I am working on Metabolomics data files for Skyline/PanoramaWeb/AutoQC. I am looking for answers for below queries.
- While installation of AutoQC Loader I am having issues with updated version, which is different from the tutorial version. I don.t see create new configuration tab or panorama settings and has different tabs like import and export. How do I use autoQC loader updated version.
- While creating QC trend report, run date tab is showing blocked and without that report doesn't proceed to next step.
Thank you, Srujana
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view message |
AutoQC Loader |
(2 responses) |
Srujana |
2020-04-07 11:59:08 |
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Hi Panorama development team,
I have recently got access to ParamaWeb. I am working on "Sharing Skyline Document" tutorial. While uploading a file, "IMPORT WAITING" prompt appearin. And in Panorama page also i am seeing the same information. Could you please suggeste me if I need to get additonal acess to use this tutorial? As mentioned in the tutorial overiwe section, I didnt fid a TOTUORIAL folder but I have created a folder in Icahn Scool of Medicine page. I have a uploaded word document with screen shots.
Thanks- Srujana
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SG_Panorama_support.docx |
view message |
Upload raw data |
(1 response) |
ferdinando cerciello |
2020-04-04 09:15:40 |
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Hi Vagisha,
I have another question: I m now trying to upload the raw data related to the Skyline files, but when I go to the Raw Data page it tells it is not possible to upload data. Indeed I can t drop and drag anything or even upload by browsing to them. Also, I can t create subfolders. The error report is something like...file root web to this part could not be found.
Is there any setting I need to change in the file settings in order to be able to upload the raw files?
Thank you Ferdinando
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view message |
Errror: Aminoacid value |
(2 responses) |
ferdinando cerciello |
2020-03-30 14:43:09 |
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Hi all, I m trying to upload my files on panorama, but when submitting the import button, I get this error back: AminoAcid: value is too long for column "AminoAcid", a maximum length of 1 is allowed. Supplied value was 4 characters long. I can t understand to what it refers. I tried by shortening the name of the files, but it did not help. The aminoacids within the files are normally visible within the Skyline file.
Thank you Ferdinando
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view message |
Error configuring new instrument in Panorama |
(1 response) |
Taher Elgierari |
2020-03-26 14:05:14 |
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just configured a new instrument in Panorama, that went fine, but when configuring the AutoQC I kept getting the an error saying the folder i entered is not a Panorama folder, i confirmed the folder directory and name matches what in Panorama. thanks. taher
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Panorama.PNG |
view message |
Error when adjusting |
(4 responses) |
Taher Elgierari |
2020-02-07 17:35:49 |
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when using "Monitoring molecular contaminants and interferences in proteomic data sets" document i get error every time i try to adjust the resolution to accommodate Sciex 6600 instruments , it is fixed on orbtrap 60,000 at 400, is there a way to change it, or it doesn't matter sense it contains MS1 data only. the link to the document; https://panoramaweb.org/contaminants.url
thanks. taher
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view message |
Errors uploading XL data to Panorama |
|
azelter |
2020-01-10 14:53:40 |
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I have successfully uploaded one skyline document to Panorama which contains XL targets created by Nick's crosslinker tool. Two subsequent runs failed with different errors (see below).
Any insight into what the problem might be would be much appreciated! Thanks very much for your help!
--
10 Jan 2020 14:36:18,683 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
10 Jan 2020 14:36:18,684 ERROR: SqlExecutor.execute(); uncategorized SQLException for SQL []; SQL state [25P02]; error code [0]; ERROR: current transaction is aborted, commands ignored until end of transaction block; nested exception is org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
Caused by: org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "uix_auditlogentry_document"
Detail: Key (documentguid, entryhash)=(f13e38db-d3d1-483f-9157-a8ed31613ac8, R5jGBMHhj59meKIGY6s1/mns8Z4=) already exists.
--
10 Jan 2020 14:44:39,469 INFO : Done parsing Skyline document.
10 Jan 2020 14:44:41,209 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
10 Jan 2020 14:44:41,209 ERROR: Index 0 out of bounds for length 0
--
|
view message |
Issue with Unimod modification IDs needed for ProteomeXchange submission |
(5 responses) |
j hamey |
2019-12-10 13:39:36 |
|
Hi there,
I'm having an issue submitting data to Panorama public that I would like to get a ProteomeXchange ID for.
In order to analyse my data in Skyline, I had to create custom modifications. In particular, I created two modifications that are essentially the same as two existing unimod modifications (accessions 1291 and 298), but which were not findable in Skyline.
The submission process says that the modifications must have a Unimod ID in order to get a ProteomeXchange ID, and that the remedy is to edit the modifications in Skyline and reupload everything. However, this seems like it would be untenable given the number of Skyline documents and peptides in my dataset, and the modification names in Unimod would also make the dataset more confusing. Is it possible to simply associate the data with the two relevant Unimod modifications rather than change every instance of these modifications?
Thank you for your help.
Josh
|
view message |
Not possible to view chromatogram library |
(2 responses) |
Andreas Hober |
2019-11-26 07:19:17 |
|
Hi, I have been working quite a lot with Panorama for building chromatogram libraries and it has worked splendidly. However, the libraries that I have downloaded lately have all been corrupt in some way and I cannot view the chromatograms in Skylines, but I can clearly view them in the corresponding Panorama project.
Is there anything I can do in order to solve this or is there some issue which the creation of the .clib on the server? I have attached the error message that I receive below.
Best regards Andreas
Installation ID: cfcf80a6-7631-4cba-8bf1-6cbb20a1ff50
Exception type: NullReferenceException
Error message: Object reference not set to an instance of an object.
--------------------
Stack trace:
at pwiz.Skyline.Model.Lib.ChromLib.ChromatogramLibrary.ReadChromatogram(ChromLibSpectrumInfo info) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\ChromLib\ChromatogramLibrary.cs:line 96
at pwiz.Skyline.Model.Lib.CachedLibrary`1.LoadChromatogramData(Object spectrumKey) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\Library.cs:line 1044
at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateUI(Boolean selectionChanged) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 697
at pwiz.Skyline.SettingsUI.ViewLibraryDlg.listPeptide_SelectedIndexChanged(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 1070
at System.Windows.Forms.ListBox.OnSelectedIndexChanged(EventArgs e)
at System.Windows.Forms.ListBox.set_SelectedIndex(Int32 value)
at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateListPeptide(Int32 selectPeptideIndex) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 512
at pwiz.Skyline.SettingsUI.ViewLibraryDlg.UpdateViewLibraryDlg() in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 311
at pwiz.Skyline.SettingsUI.ViewLibraryDlg.ViewLibraryDlg_Load(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\ViewLibraryDlg.cs:line 222
at System.Windows.Forms.Form.OnLoad(EventArgs e)
at pwiz.Skyline.Util.FormEx.OnLoad(EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\FormEx.cs:line 198
at System.Windows.Forms.Form.OnCreateControl()
at System.Windows.Forms.Control.CreateControl(Boolean fIgnoreVisible)
at System.Windows.Forms.Control.CreateControl()
at System.Windows.Forms.Control.WmShowWindow(Message& m)
at System.Windows.Forms.Control.WndProc(Message& m)
at System.Windows.Forms.Form.WmShowWindow(Message& m)
at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
Exception caught at:
at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
at System.Windows.Forms.Control.WndProcException(Exception e)
at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
at System.Windows.Forms.SafeNativeMethods.ShowWindow(HandleRef hWnd, Int32 nCmdShow)
at System.Windows.Forms.Control.SetVisibleCore(Boolean value)
at System.Windows.Forms.Form.SetVisibleCore(Boolean value)
at System.Windows.Forms.Form.Show(IWin32Window owner)
at pwiz.Skyline.SkylineWindow.OpenLibraryExplorer(String libraryName) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2921
at pwiz.Skyline.SkylineWindow.ViewSpectralLibraries() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2871
at pwiz.Skyline.SkylineWindow.spectralLibrariesToolStripMenuItem_Click(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 2840
at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
at System.Windows.Forms.Control.WndProc(Message& m)
at System.Windows.Forms.ToolStrip.WndProc(Message& m)
at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
at pwiz.Skyline.Program.Main(String[] args) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Program.cs:line 305
|
view message |
Upload to Panorama Public |
|
michael plank |
2019-10-01 11:19:41 |
|
Hi,
could anyone please tell me what 'Drag and drop to the files browser in the Raw Data tab to upload files' means when trying to do an upload to Panorama Public. (I encounter this after selecting 'Submit'.) When I press 'Upload Raw Data', I always get reverted to the project folder, but I don`t see a Raw Data tab'.
Thanks.
|
view message |
Folder on Panorama |
(2 responses) |
romeally |
2019-09-20 12:00:16 |
|
I am trying to set up AutoQC and when I input the path to my folder on Panorama it says it is not a Panorama folder. I can get on Panorama and navigate to the folder so it does exist. Do AutoQC folders need a special designation? I am attaching the error I received as a screen capture. How do I connect to my folder? Thanks, Bob O'Meally
|
PanoramaSetupQuestion.docx |
view message |
Submit button is missing |
(2 responses) |
Sabrina Geisslitz |
2019-09-16 23:32:54 |
|
I already submitted data of another project to Panorama. I think, this time, I did it exactly the same way. I created a folder and two subfolders. In the main folder, I created the "targeted MS experiment" and included the subfolders. I checked the folder permissions. They are exactly the same as for the previous project. I also checked that the folders are "Panorama" folders and not Collaboration folders. But now, the submit button is missing. I used Skyline version 19.1.0.193 and Mozilla Firefox. I hope you can help me that I can submit my data. Sabrina
|
SubmitButtonMissing.docx |
view message |
Updating chromatogram libraries with metadata |
(1 response) |
Andreas Hober |
2019-08-19 07:52:32 |
|
Hi, I was only wondering if it would be possible to update chromatogram libraries on Panorama with metadata from e.g. a background proteome. It would be very useful when looking at the overviews for protein coverage etc. I am currently working with quite a few Skyline files where all the proteins are named based on the standards that have been used for the method development and it would be great if I would be able to add a background proteome for grouping of the peptides once they have been added to assay project on Panorama, since now I have quite a few "proteins" which actually map towards the same actual protein.
Best regards Andreas
|
view message |
AutoQC Loader Fails to download |
(1 response) |
romeally |
2019-08-05 13:39:41 |
|
Is anyone else getting this error when they try to run setup? I am getting the same error when I try to upgrade Skyline and I have never had any issues with that in the past. Could there be a firewall issue?
An error occurred trying to download 'http://skyline.gs.washington.edu/software/AutoQC/AutoQC.application'.
See the setup log file located at 'C:\Users\BobO\AppData\Local\Temp\VSDEF38.tmp\install.log' for more information.
|
view message |
Building assay libraries using Panorama |
|
Andreas Hober |
2019-07-24 18:11:55 |
|
Hi, I have gone through the tutorial material for storing chromatogram libraries using Panorama and that seems to be working great from a perspective of continuously expanding your assay library. I was wondering if it is possible to store iRT libraries and Collision energy libraries in a similar way using Panorama.
If not, is this something that you plan on implementing in the future?
Best regards Andreas
|
view message |
Error message when trying to view chromatogram in Panorama |
(4 responses) |
Azad Eshghi |
2019-07-04 14:29:17 |
|
Dear folks,
I've "successfully" uploaded data to Panorama, however when I try to view chromatograms I receive an error message. I have attached a screenshot of the message. Thanks in advance.
|
Panorama error message trying to view chromatogram.pdf |
view message |
AutoQC Multiple (at least 2?) Metrics Side by side?? |
(2 responses) |
Alejandro Cohen |
2019-06-07 05:47:25 |
|
Hi Panorama people!!!
Wonderful job with AutoQC, one of the best tools I've used for QC in the lab... for more than 25 years!!! (I used to plot Shewhart cotrol chart rules by hand!)
So, here suggestion that might work. Due to the generous real state of large screens, it would be very helpful if you could choose more than one metric (eg Rt and Area) side my side for each target. That would sometimes help quickly identifying and diagnosing problems, as switching from metric to metric for a big list of targets makes it hard to visualize. Of course, I could just split the browser into to screens, but then you have to synchronize scrolling (me?? ?lazy???)
You are doing a great job!!! Keep it up!!!
Alex
|
view message |
Inaccurate peak picking by AutoQC |
(1 response) |
NevesMS |
2019-06-05 13:01:16 |
|
Hello Dear,
A System Suitability workflow is being implemented in the lab but we are experience an issue with the data uploaded to Panorama using AutoQC. A few peptides are being inaccurately picked over different runs (screenshot enclosed). We double checked opening the files into Skyline and the correct peak was always present. Is it possible to provide the correct peak boundaries or scheduling the acquisition is the best option?
Best regards, Leandro
|
Picture1.png Picture2.png |
view message |
Small molecules and Panorama chromatogram libraries |
|
Chris |
2019-05-13 14:29:06 |
|
Dear Skyline and Panorama teams,
I'm interested in the chromatogram library feature of Panorama for small molecules but my small molecule assays don't seem to be compatible with the existing targeted MS runs web part. I've checked the chromatogram library file generated in the fileset folder but it appears to be empty except for the LibInfo table.
Are there current efforts underway to get chromatogram library functionality for small molecule assays on Panorama? If not, I would like to let you know that there is at least one person interested in this feature.
I originally posted this in the Skyline support section but figure this is a more appropriate place for it.
Cheers, Chris
|
view message |
Question about peptide identification |
(3 responses) |
fazeliniah |
2019-03-29 12:59:53 |
|
Hi Panorama team, We have been using the AutoQC for montoring 9 peptides (Scheduling PRM) in our standard sample. In the past few days, I have noticed that one of our peptides in the sample behave differently. Please check the attached picture. I believe that Skyline picks a wrong peak for this peptide. Is there an easy fix for this problem? I don't think this is sample related issue since we have been using an aliquot of the same standard sample for few years now. Thanks again for your work on this amazing tool. FazeliniaH
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Levey-Jennings- All Series.png |
view message |
Would you tell me how to prepare Skyline document to publish to a library folder on Panorama? |
(7 responses) |
eisuke miyauchi |
2019-03-27 19:36:50 |
|
Dear PanoramaWeb team,
I couldn't import my library downloaded from Panorama into Skyline for DIA analysis.
Would you tell me how to prepare Skyline document to publish to a library folder on Panorama?
Sincerely, Eisuke
|
view message |
Unable to upload Skyline file |
(1 response) |
Andreas Hober |
2019-03-19 09:10:13 |
|
Hi, I've been trying to upload a Skyline file to one of my Panorama projects without any success. I've tried uploading it through Skyline, as well as directly uploading the zipped Skyline file through the web interface, but neither works. I get an error message in the Data Pipeline stating "No transition match!".
The particular data set is due for submission and any help with managing to upload the data would be much appreciated.
Best regards /Andreas
|
view message |
Bruker tdf support |
(2 responses) |
Tobias Kockmann |
2019-03-04 07:16:53 |
|
Dear Panorama team,
could it be that the autoQCLoader app is not yet ready for Bruker tdf files? There is no instrument type "Bruker" selectable. Skyline-daily processes the data already and manual uploads 'to PanoramaWeb work.
Greetings, Tobi
|
view message |
Unknown error connecting to the server https://panoramaweb.org |
(4 responses) |
EvgenyKanshin |
2019-02-16 07:45:50 |
|
Dear PanoramaWeb team, since yesterday all configurations stopped working and gave this weir error message. We haven't changed anything on our side. I've attached the log file (error happened for a first time @ 2/15/2019 9:21:18 AM).
|
AutoQC.log |
view message |
Getting stuck importing data. |
(3 responses) |
tkeppel |
2019-01-18 10:39:13 |
|
Hi, I'm trying to upload results for a QC template project, but no matter if I'm uploading via the "Upload to Panorama" from within Skyline, or I try to manually drag and drop the generated .zip file or the skyline document itself, I'm getting stuck at "IMPORT WAITING". Is there a command I need to toggle to send it through to upload into my project? Thank you, Ted
|
view message |
Delete folders? |
(9 responses) |
Alejandro Cohen |
2019-01-08 11:00:27 |
|
Hi Panorama people,
I'm trying to set new folders for AutoQC of all instruments in my lab, but I cant seem to delete older folders. I get the following error when I try to delete the folders from the Folder Management page: java.lang.NullPointerException at org.labkey.pipeline.api.PipelineManager.purge(PipelineManager.java:240) at org.labkey.pipeline.PipelineModule.containerDeleted(PipelineModule.java:237) at org.labkey.api.data.ContainerManager.fireDeleteContainer(ContainerManager.java:2108) at org.labkey.api.data.ContainerManager.delete(ContainerManager.java:1573) at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(AdminController.java:6823) at org.labkey.core.admin.AdminController$DeleteFolderAction.handlePost(AdminController.java:6784) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:101) at org.labkey.api.action.FormViewAction.handleRequest(FormViewAction.java:80) at org.labkey.api.action.BaseViewAction.handleRequest(BaseViewAction.java:177) at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:482) at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:1266) at org.labkey.api.view.ViewServlet._service(ViewServlet.java:204) at org.labkey.api.view.ViewServlet.service(ViewServlet.java:131) at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:1241) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:215) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:748) request attributes LABKEY.OriginalURL = http://localhost:8080/admin/Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC/deleteFolder.view? LABKEY.StartTime = 1546973895452 LABKEY.action = deleteFolder org.springframework.web.servlet.DispatcherServlet.CONTEXT = Root WebApplicationContext: startup date [Thu Dec 20 13:54:46 PST 2018]; parent: Root WebApplicationContext LABKEY.controller = admin LABKEY.Counter = 0 org.labkey.api.util.ExceptionUtil$exception = java.lang.NullPointerException X-LABKEY-CSRF = f03e4fa741ccf58c794ea79555e0ac35 LABKEY.container = /Dalhousie University - Proteo and Metabolomics Core/QC_VelosPro/QTra5500_QC LABKEY.RequestURL = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view? LABKEY.OriginalURLHelper = /admin/Dalhousie%20University%20-%20Proteo%20and%20Metabolomics%20Core/QC_VelosPro/QTra5500_QC/deleteFolder.view?
core schema database configuration Server URL jdbc:postgresql://localhost/labkey Product Name PostgreSQL Product Version 10.3 Driver Name PostgreSQL JDBC Driver Driver Version 42.2.5
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view message |
"Missing raw data" error message when trying to publish to Panorama Public |
(2 responses) |
rschoenh |
2018-12-19 10:42:24 |
|
Hi Vagisha,
I'm trying to publish Skyline files to Panorama Public to receive reviewer logins for a manuscript submission, but Panorama is giving me an error message stating that there are "Missing raw data." It's listing the Skyline document .zip files alongside the Missing raw data .wiff files. I thought at first that this was the case because the Skyline files I uploaded were located in a different file folder (on my computer) than the wiff files, but I tested that by adding the wiff file to the folder that contained the Skyline file and uploading the data to Panorama again, but it still gave me the same error message. It's also curious that for this particular Skyline file, it's listing only 1 wiff file as missing, whereas there are data from 2 wiff files in the Skyline file.
Thanks so much in advance for your time and help!
Best, Regine
|
view message |
[12/9/2018 10:40:31 AM] User tobias.kockmann@fgcz.ethz.ch does not have permissions to upload to the Panorama folder /Functional Genomics Center Zurich - Proteomics & Protein Analysis Group/Qcloud/QEXACTIVEHF_2 |
(4 responses) |
Tobias Kockmann |
2018-12-09 04:33:22 |
|
Dear Panorama support,
our autoQC loader client reports:
[12/9/2018 10:40:31 AM] User tobias.kockmann@fgcz.ethz.ch does not have permissions to upload to the Panorama folder /Functional Genomics Center Zurich - Proteomics & Protein Analysis Group/Qcloud/QEXACTIVEHF_2
Did somebody mess with my Panorama account? I have used it to upload data for months and now all of a sudden I am lacking permissions?
Greetings, Tobi
|
view message |
Can we get logs? |
(2 responses) |
eisuke miyauchi |
2018-11-26 18:28:27 |
|
Dear PanoramaWeb team,
Can we get logs (ex. operation logs, event logs, and so on) in order to detect unauthorized accesses?
Sincerely, Eisuke
|
view message |
Account permissions |
(2 responses) |
Klemens Fröhlich |
2018-11-14 09:57:41 |
|
Dear PanoramaWeb Team, I was part of the Skyline Course in August this year. We there got an account from Vagisha Sharma. I now want to use AutoQC to establish an automated QC report system for our targeted peptide panels on a TSQ vantage. However, I have great troubles following tutorials and webinars on that matter, because I do not seem to have a GROUP in panorama? I cannot access any projects of my own which makes it impossible for me to create folders (If I hover over the HOME directory in the upper left corner of the website I simply do not see any "add folder" button). I also cannot manage any permissions as described.
As already mentioned I think this could be linked to the fact that I do not have any GROUP status in my account.
I would appreciate any feedback on the matter. I would be perfectly happy with an account on the MacCoss Server as described on the sharing_documents#subfolder page.
Best, Klemens
|
view message |
Inquiring about PanoramaWeb |
(2 responses) |
eisuke miyauchi |
2018-10-29 01:07:11 |
|
I have 4 questions in order to operate PanoramaWeb in our company.
1. Has the data remaining on the cloud definitely erased to prevent reuse or misuse by a third party after withdrawing from PanoramaWeb?
2. Can University of Washington access and use our data on the cloud?
3. How much storage capacity of the cloud?
4. What will become of the data on the cloud when PanoramaWeb is terminated? Can Spectral libraries exported from PanoramaWeb be used in other softwares?
|
view message |
File name information shown above a chromatogram |
(2 responses) |
rschoenh |
2018-10-24 11:01:28 |
|
Hello,
I'm trying to simplify the information that's shown above the peptide chromatograms for targeted MS runs. At the moment the information seems to include Sample or Replicate name, wiff file name, date of acquisition, peptide sequence, etc. I'm wondering if there is a way to not show the wiff file names, since mine happened to be quite long and it makes the information a bit convoluted.
Thanks very much in advance for your help! Best, Regine
|
view message |
How to Download All Data Points for Plots? |
(1 response) |
loffredoj |
2018-10-18 15:18:13 |
|
Is it possible to download the data points on the 'Peak Area' Metric for all the uploaded files of each ion being targeted, using PanoramaWeb? (as a .txt or .xls) The downloaded data points would have fields like the name of each ion and the Peak Area, for a specific date. I uploaded a picture of the plot I am referring to. Our data is uploaded from TripleTOF 6600 systems and have been uploaded using the AutoQC client, and I am using Google Chrome to view PanoramaWeb.
Best, Jeremy
|
PeakArea_Plot.PNG |
view message |
QC Plots are not Displayed |
(7 responses) |
s merker |
2018-10-12 02:10:20 |
|
Dear Panorama team,
first of all, thank you so much for the great work you are doing! We have recently implemented QC for our QTrap 5500 system based on Skyline and Panorama employing the AutoQC client. I have to say that it greatly facilitates the workflow compared to manual data inspection in Skyline. However, since yesterday no QC Plots can be displayed on our dashboard ("no data to plot"). However, samples are being successfully uploaded into the specified Skyline document and also to Panorama, according to the AutoQC log (new sample names also appear in the QC summary, just the plots are gone, s. attached screenshot). When I enter the public Panorama project "U of Melbourne - Proteomics Facility", I can see and manipulate QC Plots there, so this does not seem to be a browser or a general issue. We use regular Skyline release 4.1.0.18169 combined with AutoQC Loader 1.1.0.11725, OS is Windows 7 Professional, 64-bit. Restarting the relevant configuration in the loader did not help. I would very much appreciate any suggestions since we are quite new to Panorama and have never encountered that issue before.
Best regards,
Roman
|
QC_Plots_Sakson.tif |
view message |
Adding Users - No Email Received |
(2 responses) |
chapmanj |
2018-10-05 09:38:59 |
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Hello
I added my 2 lab members as users to our laboratory QC Panorama Project and in the instructions it says they should receive an email inviting them to create an account. I initially did this on 9/14/18 and they never received any communication. We have checked all junk and spam folders. Any suggestions or work arounds to get them up and running so I am not the sole person able to access our AutoQC?
Thank you for your help! :) JRC
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view message |
Raw files not recognized in submitted Panorama experiment |
(3 responses) |
Laura Spencer |
2018-09-27 12:37:38 |
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I'm uploading an SRM experiment (Skyline project file, description, raw files). I uploaded the raw files but they are not being recognized, as it appears the associated raw file names linked to the Skyline project file all have some additional text added to the file names. Is there any way to get my uploaded raw files linked to the skyline project in Panorama? Thanks!
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view message |
Public Panorama for DIA raw files? |
(3 responses) |
Steve Sweet |
2018-08-21 06:48:36 |
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Hi Panorama Support,
I see it is possible to upload raw files to Panorama, however the Public Panorama projects I clicked on only seemed to have .sky.zip files (presumably the Skyline results files). And the tutorial for Panorama Public doesn’t mention raw files. Is it preferable to use something like PRIDE at EMBL to upload raw files, or can raw files be uploaded alongside Skyline files in Panorama Public?
Our DIA raw files are fairly large: 20 GB in total; 0.5 to 1.5 GB per raw file.
Thanks,
Steve
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view message |
ETD Reagent Ion Signal |
(2 responses) |
brown459 |
2018-08-08 05:51:56 |
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Hello-
I was wondering if there were a way to assay the ETD reagent ion signal on a Thermo Fusion Lumos using AutoQC. Currently we look through the individual scan headers output checking the "number of LM found" and the "LM correction (ppm)." This assay requires the instrument method to run Easy-IC. While we have a script that completes this task, it requires a little bit more work than we would like. The reason we want this installed is because we can clean the cathode (ETD source) and restore reagent ion signal when it decays-- increasing our LM accuracy and increasing our signal ETD fragment efficacy. Furthermore, this last point seems to be a great use of the AutoQC system.
Cheers,
CJB
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view message |
QC Plot Headers |
(3 responses) |
brown459 |
2018-08-07 06:30:26 |
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Is there a way to change the QC plot headers (typically a peptide sequence) to a m/z? Or have it write out "PEPTIDE, m/z" as the header?
Thanks,
CJB
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view message |
Instrument type |
(2 responses) |
nicakruh |
2018-08-06 10:02:46 |
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I am adding a data set to Panorama and having issues with the Instrument field. There is no drop-down list and it is not accepting my manual entry for Waters Xevo Tq-S. Can you clarify the correct way to enter this instrument so that I don't receive the error message "unrecognized instrument" when I hit submit?
Thank you!
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view message |
AutoQC and LK update? |
(2 responses) |
phains |
2018-07-16 21:56:32 |
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Our setup;
Win 10 64 bit running AutoQC: 1.1.0.11725 Skyline: 4.1.0.18169
Win server 2012, 64-bit, running LK v18.1
Since the LK update to v18.1 the uploads are failing. The files are loaded into Skyline fine, but then the upload to the server LK fails.
I’ve attached a number of log files; AutoQC_log_PC6.txt the log for one specific configuration. AutoQCProgram.log the log from the AutoQC install directory LK_log.txt the log from LK for the specific AutoQC configuration above
Any help on this would be appreciated.
Peter
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AutoQC_log_PC6.txt AutoQCProgram.log LK_log.txt |
view message |
AutoQC importing replicates with the same name |
(3 responses) |
bonnie baker |
2018-07-11 12:12:03 |
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I'm trying to use AutoQC-daily to control chart our daily instrument QC data in Panorama. Each day we submit the same batch, but change the date on the output *.wiff file. As such, the QC data all has the same name and the AutoQC log file shows the error: "The replicate MRM 100ng_mL 001 already exists in the given document and the --import-append option is not specified. The replicate will not be added to the document."
Is there a workaround?
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view message |
feature request |
(1 response) |
Tobias Kockmann |
2018-07-11 07:07:40 |
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Hi Panorama team,
as discussed at the skyline user meeting I would like to suggest some new features for Panorama + autoQC. I am not sure how other people use this tool, but our sample for system suitability testing contains iRT peptides. We accordingly use iRT regression as a performance measure, since the parameter estimates (slope and intercept) tell us if our LCs really deliver the commanded gradients. Unfortunately, we always have to do this offline, since Panorama does not monitor these parameters, although the skyline doc records the iRT regression on the fly. What about including diagnostic plots for RT regression in Panorama?
Another feature request: Panorama ignores the protein/peptide list context of targets. Our targets lists during autoQC runs contain a mixture of matrix peptides (BSA) and iRTs. Unfortunately, they are all displayed alike and in alphabetic order. Some sort of filtering/grouping according to peptide list/protein context would help very much! Also sorting according to hydrophobicity or iRT value would be a cool feature.
Let me know what you think about my suggestions, Tobi
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view message |
running autoQC loader from the command line |
(3 responses) |
Tobias Kockmann |
2018-07-06 01:38:55 |
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Hi Panorama support,
is it possible to run the autoQC loader application from the command line? We would like to script the complete autoQC pipeline and the loader application seems to be the missing part in the pipeline.
Greetings, Tobi
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view message |
AutoQC and *.wiff files |
(2 responses) |
bonnie baker |
2018-06-28 08:24:42 |
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I'm just getting started using AutoQC to load QC data into skyline. I successfully created a configuration but it appears that AutoQC is only loading the first scan into my skyline file. Is there anyway to get it to load more than one scan from a *.wiff file? Better yet, can I add just the scans from the *.wiff file that contain a particular text string in their name?
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view message |
AutoQC suggestions |
(7 responses) |
Alejandro Cohen |
2018-05-31 10:41:12 |
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Hi Panorama people,
I'm using AutoQC and Loader, and I am marveled by it.... a long overdue solution to QC in MS laboratories. I'm using it with an aliquoted BSA digest using MS1 filtering on Skyline (VeloPro acquisition) and this has given me a great tool to assess the overall LC-MS performance prior to running real samples, KUDOS to ALL your team!!!
Now my suggestions:
-Is it possible to add to the QC plots types an additional parameter such as Xcorr or some other output parameter to assess the MSMS quality for DDA acquisitions?? This would be great!!! You already now the sequence of the target peptides, and it is likely you can pull out the MSMS for that precursor in each file. If you could monitor the additional parameter to follow over time, it would be a great source to assess the 'health' of the MSMS.
-Have you considered selling/distributing a QC sample (protein digest?) to be used as an external QC like done typically in clinical labs? It would be great to not only have internal QCs, but also external QCs and evaluate how your instrument is performing compared to identical (or not) instruments in other labs (anonymous). I imagine the huge variability as everyone is using different LC conditions, but if this could be minimally standardized, it could be a source of precious information to evaluate inter-laboratory variability
Cheers
Alex
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view message |
administrator privilege |
(4 responses) |
jquijada |
2018-05-14 11:39:31 |
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Hi Panorama Team,
I am a new user of Panorama, and I received my Panorama account around a week ago. I have been trying to create folder and invite people, but I do not find the icons that are shown in the tutorial for these functions. Therefore, I wonder if I could have administrator privilege or how can I request them.
My email: jquijada@stanford.edu
My lab folder is: Stanford U - Snyder Lab
Please, let me know if you need any additional information.
Best regards,
Jeniffer
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view message |
AutoQC Loader |
(2 responses) |
Alejandro Cohen |
2018-05-03 12:07:28 |
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Hi Skyline/Panorama people!
I'm staring my on QC using AutoQC on Panorama, Skyline and AutoQCLoader. I'm following the tutorial, but when I run my Configuration on Loader I get the following message. I guess the Sklyline file generated on Daily is to 'new' for this version of Loader?? Could you tell me if I'm doing something wrong or an update is available??? Below the Log on AutoQC Loader.
Thanks!!!
Alex
[03/05/2018 3:50:24 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User:
Created: 03/05/20183:50 PM
Modified: 03/05/20183:50 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Not publishing to a Panorama server.
[03/05/2018 3:50:24 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 3:50:24 PM] Running SkylineRunner.exe with args:
[03/05/2018 3:50:24 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 3:50:31 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 3:50:31 PM] Opening file...
[03/05/2018 3:50:31 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 3:50:31 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 3:50:31 PM] Exiting...
[03/05/2018 3:50:31 PM] SkylineRunner.exe exited successfully.
[03/05/2018 3:50:31 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 3:50:31 PM] ERROR: Error importing file.
[03/05/2018 3:52:15 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User:
Created: 03/05/20183:50 PM
Modified: 03/05/20183:50 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Not publishing to a Panorama server.
[03/05/2018 3:52:15 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 3:52:15 PM] Running SkylineRunner.exe with args:
[03/05/2018 3:52:15 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 3:52:17 PM] The name 'AcquisitionTimes' already exists.
[03/05/2018 3:52:17 PM] Resolving conflicts by overwriting.
[03/05/2018 3:52:17 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 3:52:17 PM] Opening file...
[03/05/2018 3:52:17 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 3:52:17 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 3:52:17 PM] Exiting...
[03/05/2018 3:52:17 PM] SkylineRunner.exe exited successfully.
[03/05/2018 3:52:17 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 3:52:17 PM] ERROR: Error importing file.
[03/05/2018 3:52:21 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User:
Created: 03/05/20183:50 PM
Modified: 03/05/20183:50 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Not publishing to a Panorama server.
[03/05/2018 3:52:21 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 3:52:21 PM] Running SkylineRunner.exe with args:
[03/05/2018 3:52:21 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 3:52:23 PM] The name 'AcquisitionTimes' already exists.
[03/05/2018 3:52:23 PM] Resolving conflicts by overwriting.
[03/05/2018 3:52:23 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 3:52:23 PM] Opening file...
[03/05/2018 3:52:23 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 3:52:23 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 3:52:23 PM] Exiting...
[03/05/2018 3:52:23 PM] SkylineRunner.exe exited successfully.
[03/05/2018 3:52:23 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 3:52:23 PM] ERROR: Error importing file.
[03/05/2018 3:57:08 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User: alejandro.cohen@dal.ca
Created: 03/05/20183:50 PM
Modified: 03/05/20183:56 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Panorama server URL: https://panoramaweb.org/
Panorama user email: alejandro.cohen@dal.ca
Panorama folder: /Dalhousie University - Proteo and Metabolomics Core/VelosPRO_QC
[03/05/2018 3:57:10 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 3:57:10 PM] Running SkylineRunner.exe with args:
[03/05/2018 3:57:10 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 3:57:12 PM] The name 'AcquisitionTimes' already exists.
[03/05/2018 3:57:12 PM] Resolving conflicts by overwriting.
[03/05/2018 3:57:12 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 3:57:12 PM] Opening file...
[03/05/2018 3:57:12 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 3:57:12 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 3:57:12 PM] Exiting...
[03/05/2018 3:57:12 PM] SkylineRunner.exe exited successfully.
[03/05/2018 3:57:12 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 3:57:12 PM] ERROR: Error importing file.
[03/05/2018 3:58:09 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User: alejandro.cohen@dal.ca
Created: 03/05/20183:50 PM
Modified: 03/05/20183:56 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Panorama server URL: https://panoramaweb.org/
Panorama user email: alejandro.cohen@dal.ca
Panorama folder: /Dalhousie University - Proteo and Metabolomics Core/VelosPRO_QC
[03/05/2018 3:58:11 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 3:58:11 PM] Running SkylineRunner.exe with args:
[03/05/2018 3:58:11 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 3:58:12 PM] The name 'AcquisitionTimes' already exists.
[03/05/2018 3:58:12 PM] Resolving conflicts by overwriting.
[03/05/2018 3:58:12 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 3:58:12 PM] Opening file...
[03/05/2018 3:58:12 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 3:58:12 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 3:58:12 PM] Exiting...
[03/05/2018 3:58:12 PM] SkylineRunner.exe exited successfully.
[03/05/2018 3:58:12 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 3:58:12 PM] ERROR: Error importing file.
[03/05/2018 4:03:31 PM] Logging initialized...
Name: VelosPro_BSA_QC
Enabled: True
Panorama User: alejandro.cohen@dal.ca
Created: 03/05/20183:50 PM
Modified: 03/05/20183:56 PM
Main Settings
Skyline file: C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
Folder to watch: Z:\VELOS\BSA_Std_250ng
Include subfolders: False
Filter Type: All
Instrument: Thermo
Results window: 360 days
Acquisition time: 90 minutes
Panorama Settings
Panorama server URL: https://panoramaweb.org/
Panorama user email: alejandro.cohen@dal.ca
Panorama folder: /Dalhousie University - Proteo and Metabolomics Core/VelosPRO_QC
[03/05/2018 4:03:33 PM] Getting the acquisition date on the newest file imported into the Skyline document.
[03/05/2018 4:03:33 PM] Running SkylineRunner.exe with args:
[03/05/2018 4:03:33 PM] --in="C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky" --report-conflict-resolution=overwrite --report-add="C:\Users\Dal U\AppData\Local\Apps\2.0\7CE8A91Z.HPK\79DBY68V.WJ3\auto..tion_e4141a2a22107248_0001.0001_57bf953e1a79aace\FileAcquisitionTime.skyr" --report-name="AcquisitionTimes" --report-file="C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv"
[03/05/2018 4:03:35 PM] The name 'AcquisitionTimes' already exists.
[03/05/2018 4:03:35 PM] Resolving conflicts by overwriting.
[03/05/2018 4:03:35 PM] Success! Imported Reports from FileAcquisitionTime
[03/05/2018 4:03:35 PM] Opening file...
[03/05/2018 4:03:35 PM] ERROR: Error: There was an error opening the file C:\Users\Dal U\Documents\Skyline Libraries\VelosPro_BSA_QC.sky
[03/05/2018 4:03:35 PM] The document format version 4.11 is newer than the version 3.7 supported by Skyline (64-bit) 3.7.0.11317.
[03/05/2018 4:03:35 PM] Exiting...
[03/05/2018 4:03:35 PM] SkylineRunner.exe exited successfully.
[03/05/2018 4:03:35 PM] ERROR: Could not find report outout C:\Users\Dal U\Documents\Skyline Libraries\AcquisitionTimes.csv
[03/05/2018 4:03:35 PM] ERROR: Error importing file.
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view message |
'MIDAS_QC_Hela_iRT' library not found in settings. |
(1 response) |
Cheng Huang |
2018-04-22 21:25:38 |
|
Hi:
I am trying to publish the MRM result, but keep on getting the same error message. I have double checked 'MIDAS_QC_Hela_iRT' is ticked in the library settings, although I have no idea where it is from. Could you please have a look?
Thank you very much for your help.
Cheers
Cheng
SHOW FULL LOG FILE
22 Apr 2018 19:54:55,579 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
22 Apr 2018 19:54:55,582 INFO : Starting to import Skyline document from QC_Hela_iRT_2018-04-23_12-54-42.sky.zip
22 Apr 2018 19:54:55,582 INFO : Expanding iRT_C18_Calibr.irtdb
22 Apr 2018 19:54:55,583 INFO : Expanding Hela_iRT.blib
22 Apr 2018 19:54:55,585 INFO : Expanding QC_Hela_iRT.midas
22 Apr 2018 19:54:56,678 INFO : Expanding QC_Hela_iRT.skyd
22 Apr 2018 19:54:56,685 INFO : Expanding QC_Hela_iRT.sky.view
22 Apr 2018 19:54:56,686 INFO : Expanding QC_Hela_iRT.sky
22 Apr 2018 19:54:56,734 INFO : Inserting iRT-C18 Standard Peptides
22 Apr 2018 19:55:00,114 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
22 Apr 2018 19:55:00,115 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - QC_Hela_iRT_2018-04-23_12-54-42.sky.zip
org.labkey.targetedms.PanoramaBadDataException: 'MIDAS_QC_Hela_iRT' library not found in settings.
|
view message |
Stay signed in? |
(2 responses) |
socall |
2018-04-18 00:05:52 |
|
Hi,
I'm trying to grab screenshots of my QC pages so that MS techies can be sent a regular email suggesting they check the page, and adding a preview. However I need to sign in everytime I reopen a browser (or get a script to do it). Is there a way I can stay signed in on a particular machine?
Alternatively, is there a permission I can set for my pages that allows them to be viewed without being signed in?
Many thanks,
Sean
|
view message |
AutoQC unable to verify username and password |
(2 responses) |
Large Mol Quantitation Group |
2018-04-03 12:08:39 |
|
My AutoQC has been unable to verify username and password to publish to Panorama. I am able to use the same username and password to log into the panorama website, and I have tried deleting, and retyping the username password a couple of times now, but with no success. I have attached the log file here.
Skyline Ver 3.7.0.11317
AutoQC Loader 1.1.0.11725
|
Panorama log.txt |
view message |
Sharing dataset for reviewer |
(2 responses) |
Alok |
2018-03-20 16:22:23 |
|
Hi PanoramaWeb team,
I uploaded a dataset to the PanoramaWeb and it hasn't been made publicly available yet. We are about to submit a manuscript for publication. Is there a way by which we can give access to this dataset to reviewers without making it publicly available?
Thanks,
Alok
|
view message |
Delete folder |
(1 response) |
Alok |
2018-03-15 22:27:14 |
|
Hi,
While trying to get my head around using PanoramaWeb, I created couple of subfolders accidentally that needs to be removed. I looked for an option to delete those folders but I can't find an option. I confirm that I am administration of the the parent folder and those subfolders.
Thanks,
Alok
|
view message |
Unknown error attempting to publish to Panorama |
(1 response) |
fazeliniah |
2018-02-12 07:29:35 |
|
Hi Panorama Team,
Our AutoQC has stopped uploading the results to PanoramaWeb. There is a remote server error (The remote server returned an error: (404) Not Found.). I 'd appreciate it if you could take a look. We are using skyline daily with the updated version of AutoQC. I have attached the log file for your review.
Thanks
Hossein
|
panorama_log.txt |
view message |
AutoQC 404 error |
(1 response) |
socall |
2018-02-11 22:02:48 |
|
Hi,
I'm trying to get AutoQC to talk to Panorama. The folder I'm trying to write to is here: https://panoramaweb.org/project/U%20of%20Melbourne%20%E2%80%93%20Proteomics%20Facility/Orbitrab_Elite_QC/begin.view? (Yes I managed to spell Orbitrap with a 'b' when making the folder!)
For project folder name in the panorama settings in AutoQC i've tried "U of Melbourne – Proteomics Facility/Orbitrab_Elite_QC" , "project/U of Melbourne – Proteomics Facility/Orbitrab_Elite_QC", "U%20of%20Melbourne%20%E2%80%93%20Proteomics%20Facility/Orbitrab_Elite_QC", and just about everything else I can think of, but no joy.
The error I get is "The remote server returned and error: (404) Not Found", so I assume the address is wrong somehow.
Any ideas? Thanks, Sean
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view message |
Notification alert in AutoQC |
(1 response) |
fazeliniah |
2017-12-12 13:12:01 |
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Hi Panorama Team,
Is it possible to set up notification alert for AutoQC? Ideally, we would like to get notified immediately (text or email) if some of our numbers are below user-specified values?
Thanks
Hossein
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view message |
Panorama Upload Error |
(3 responses) |
mdowns2 |
2017-12-12 11:07:24 |
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Hi Panorama Support Team,
I recently attempted to upload a new Skyline document to one of our PanoramaWeb folders, but I received the error below. Could you please help me figure out what is causing the issue?
Thank you,
Melanie
12 Dec 2017 08:54:30,597 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
12 Dec 2017 08:54:30,600 INFO : Starting to import Skyline document from 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD_2017-12-12_10-53-51.sky.zip
12 Dec 2017 08:54:30,600 INFO : Expanding 2016-11-11_LysozymeDiscoForPRM.blib
12 Dec 2017 08:54:30,601 INFO : Expanding 2016-11-11_LysozymeDiscoForPRM.redundant.blib
12 Dec 2017 08:54:30,603 INFO : Expanding 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD.skyd
12 Dec 2017 08:54:30,859 INFO : Expanding 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD.sky.view
12 Dec 2017 08:54:30,859 INFO : Expanding 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD.sky
12 Dec 2017 08:54:30,867 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.62
12 Dec 2017 08:54:32,739 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
12 Dec 2017 08:54:32,741 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - 2017-12-06_Lysozyme-Wine_Spikes_pH_optimization_MD_2017-12-12_10-53-51.sky.zip
org.labkey.api.query.RuntimeValidationException: name: Value is too long for column 'name', a maximum length of 200 is allowed.
Caused by: name: Value is too long for column 'name', a maximum length of 200 is allowed.
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view message |
multiple users |
(1 response) |
fazeliniah |
2017-11-29 13:12:24 |
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Hi Panorama team,
We have started to use AutoQC for our instruments. Thanks for this really amazing tool.
Is there a way to allow multiple people in our lab view the results of QC using their own login information? Ideally, I would like to add 2-3 users so they can view the results on PanoramaWeb.
Thanks
Hossein
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view message |
Import waiting indefinitely without anything happening |
(3 responses) |
dkueltz |
2017-11-29 08:14:16 |
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Hi Vagisha,
I noticed that lately it takes a very long time to upload a Skyline document to Panorama and sometimes I was not able to upload at all since the document is wait-listed infdefinetly (I have been waiting more than a day before cancelling and trying again). This is different from before when it took only a few minutes and I tried both importing directly from Skyline and via the web interface. Could you please take a look at the document that is currently "import waiting" listed and check what is wrong with it and why it does not start running?. It is in my JoLi-01 folder.
Thank you,
Dietmar
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view message |
Backwards compatibility from 3.7 to 3.6 problem |
(2 responses) |
dkueltz |
2017-11-24 22:05:27 |
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Hi,
I am trying to upload a Skyline document to Panorama. I generated the document with the latest version of Skyline daily but saved the file as Share compatible with version 3.6 to enable Panorama upload. I can ope the document now with the regular Skyline 3.7 version but still cannot upload it to Panorama despite sharing it in Skyline version 3.6 format. I get the following error:
24 Nov 2017 20:48:23,848 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.62
24 Nov 2017 20:48:28,314 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
24 Nov 2017 20:48:28,315 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - Oreoc_OmBcells_XW0003_panmin_2017-11-24_20-23-26.sky.zip
org.labkey.api.query.RuntimeValidationException: aminoacid: Value is too long for column 'aminoacid', a maximum length of 30 is allowed.
Caused by: aminoacid: Value is too long for column 'aminoacid', a maximum length of 30 is allowed.
Thanks for any help with this issue!
Dietmar
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view message |
Organizing project in Panorama |
(4 responses) |
natbat |
2017-10-31 03:47:27 |
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Hellow
I would like to organize my project in Panorama more logically but do not know how to do it.
The idea is that I would like to have several subfolders under the same project. These subfolders would correspond to different experiments separately published in the scientific journals. Therefore, they have to have different access modes.
Historically it has happend so that the first experiments already published in JProtRes-2016 were not submitted in a subfolder. Now I would like to make a separate subfolder for these data (in open access)and move them there. I created this subfolder named "Phosphopeptides in Synechocystis_SRM verification". Could you move them there?
At present, I am writing another paper, and need to submit new experiment to Panorama with the access key for reviewers. The documnet is in subfolder named "SpkG in Synechocystis 6803 GT". However, I do not see the link to publish this separate subfolder.
Or should I re-publish the whole project?
Please advise:
Can you move the old data to the specified subfolder?
How can I get the access key for the reviewers to the subfolder "SpkG in Synechocystis 6803 GT"?
Best regards
Natalia
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view message |
Small molecules in Skyline daily and Panorama upload |
(4 responses) |
Chris |
2017-10-27 02:29:10 |
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Dear Panorama support,
I've been trying to upload small molecule assays from Skyline Daily (molecules defined by chemical formula rather than defined monoisotopic mass). The assay works fine but publishing it to Panorama gives me the following error:
27 Oct 2017 02:24:23,783 ERROR: Uncaught exception in PipelineJob: (DONE) (File_name_redacted.sky.zip)
java.lang.IllegalStateException: Missing attribute mass_monoisotopic for element molecule.
I understand a workaround might be to specify the monoisotopic mass but I would prefer if the mass derived from chemical formula/adduct could be used from Skyline Daily (3.7.1.11492. Am I doing something wrong that would cause this error?
Edit: I've tried a workaround of saving the Skyline assay as non-daily v3.7 but this causes errors when trying to open it in Skyline v3.7 ("Custom ions must specify a formula or valid monoisotopic and average masses"). So this workaround is not possible.
Cheers,
Chris
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view message |
Trying to make public a dataset |
(4 responses) |
panorama sabido |
2017-10-20 01:29:48 |
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view message |
Chrom Lib "creates" new transitions |
(9 responses) |
tvaisar |
2017-10-18 06:17:12 |
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I found what I think is a critical issue - I tried to recreate the Skyline document from a Panorama clib and uploaded the clib from Panorama into Skyline - in the list of peptides and transitions, a new transition/fragment ion appeared for a peptide which was not there in the Skyline document used to create the Panorama clib. See the attached powerpoint.
It is a b-ion for which m/z is the same as a y-ion which was in the original. The correct y-ion did not show up in the peptide/transition list.
This actually happened for several peptides - this is just an example.
Tomas
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171017_Panorama_Clib_problem.pptx |
view message |
skyline crashes |
(16 responses) |
Tobias Kockmann |
2017-10-16 02:55:13 |
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Hi support,
I am getting the following error message:
Problem signature:
Problem Event Name: CLR20r3
Problem Signature 01: Skyline.exe
Problem Signature 02: 1.0.0.0
Problem Signature 03: 593f676f
Problem Signature 04: Skyline
Problem Signature 05: 1.0.0.0
Problem Signature 06: 593f676f
Problem Signature 07: 78f7
Problem Signature 08: 6
Problem Signature 09: pwiz.Skyline.Util.Assumption
OS Version: 6.3.9600.2.0.0.16.7
Locale ID: 1033
Additional Information 1: d0a3
Additional Information 2: d0a3a8f66f382cee6a91e8944b701130
Additional Information 3: 5dc3
Additional Information 4: 5dc3c9c471f74cb07429231ba6cb1284
Read our privacy statement online:
http://go.microsoft.com/fwlink/?linkid=280262
If the online privacy statement is not available, please read our privacy statement offline:
C:\Windows\system32\en-US\erofflps.txt
Can you tell me how to solve the issue?
Greetings,
Tobi
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view message |
Results not being pushed to Panorama |
(6 responses) |
pnlabsg |
2017-09-20 22:36:59 |
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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...
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view message |
Problem installing AutoQC |
(8 responses) |
wfondrie |
2017-09-19 15:09:50 |
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Hi Panorama team,
I'm having trouble installing AutoQC on our instrument computers. I get an error message saying that application download did not succeed. Just to be sure I've tried installing it alongside either Skyline-daily or the latest stable version.
When I look at the log, it seems that it times out when trying to download Skyline Runner. I've attached one of the logs here. Thank you for your help.
Best,
Will
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CAWL3D9X.log |
view message |
x axis for plots in autoQC folder are not kept const. |
(3 responses) |
Tobias Kockmann |
2017-09-14 01:02:50 |
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Levey-Jennings-EC[+57.0]C[+57.0]HGDLLEC[+57.0]ADDR.png Levey-Jennings-DGLDAASYYAPVR.png Levey-Jennings- All Series.png |
view message |
Multiple accounts on Panorama |
(1 response) |
fazeliniah |
2017-09-13 11:09:04 |
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Hi Vagisha,
I have two accounts on Panorama. One belong to our institution (I am the admin) and one is generated for me when I was at the Skyline Targeted Proteomics Course. I would like to use our institution account to share Skyline data but I can't sign out from my second account. I don't have the option to change the server name in the "Publish Document" window. Any advice? Can I ask to remove my personal account?
Thanks
Hossein
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Panorama_skyline_20170913.pptx |
view message |
Mass Accuracy of Fragment Ions |
(3 responses) |
brown459 |
2017-09-07 06:43:39 |
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Hi all-
Is there anyway that I can have a read out on panorama of the transition/fragment ion mass accuracy? Something that could allow us to determine the calibration of both parts of the fusion instrument (i.e. the mass accuracy in the OT and the IT)? This could be similar to a panorama dashboard view showing the mass accuracy of the MS1 data.
Thanks,
CJB
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view message |
There was an error uploading the document to Panorama. Stopping... |
(3 responses) |
Tobias Kockmann |
2017-08-07 01:44:09 |
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Hi support,
my AutoQC Loader 1.1.0.11134 reports this:
[8/7/2017 10:26:02 AM] Updating peak statistics
[8/7/2017 10:26:03 AM] Joining file Z:\QEXACTIVEHF_2\20170726_165_feller_autoQC_Fetuin_400amol_1.raw.skyd
[8/7/2017 10:26:03 AM] Saving file...
[8/7/2017 10:26:04 AM] File autoQC_HF2_centroided_mode.sky saved.
[8/7/2017 10:26:07 AM] Uploaded 1.11 MB of 15.56 MB
[8/7/2017 10:26:09 AM] 100% - Uploaded 15.56 MB of 15.56 MB
[8/7/2017 10:26:10 AM] Renaming temporary file on server
[8/7/2017 10:26:32 AM] ERROR: Error: Exception of type 'pwiz.Skyline.Util.PanoramaImportErrorException' was thrown.
[8/7/2017 10:26:32 AM] An error occurred on the Panorama server ( https://panoramaweb.org/) importing the file.
[8/7/2017 10:26:32 AM] ERROR: Error details can be found at https://panoramaweb.org/labkey/pipeline-status/Functional Genomics Center Zurich - Proteomics %26 Protein Analysis Group/autoQC Server/QEXACTIVEHF2/details.view?rowId=20026
[8/7/2017 10:26:32 AM] ERROR: SkylineRunner.exe exited with code 0. Panorama upload failed.
[8/7/2017 10:26:32 AM] Finished importing existing files...
[8/7/2017 10:26:32 AM] ERROR: There was an error uploading the document to Panorama. Stopping...
What can I do? I restarted the corresponding config. No change.
Greetings,
Tobi
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Screen Shot 2017-08-07 at 10.32.17.png |
view message |
set password does nothing |
(5 responses) |
Tobias Kockmann |
2017-07-20 23:44:11 |
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Hi there,
I am trying to set a pw for a new user, but nothing happens after hitting the return key. Who should I contact?
A more general question: We are using autoQC and during the test phase all uploading of data was done using my personal account. Now, I would like to release the system to the whole group. Which user status is required for
- uploading data to autoQC folders?
- adding annotations/guide sets?
- viewing the data
Greetings,
Tobi
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view message |
Upload error |
(5 responses) |
phains |
2017-07-18 18:26:55 |
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Hi,
I am having similar issues to those already described. First off, I'm using LabKey 17.2 (just upgraded, but the issues were occurring with the prior version), AutoQC is V 1.1.0.10626 and Skyline is V3.7.0.10940, all 64-bit, Win 10 for AutoQC and Skyline or Win server 2012 for LabKey.
All my current AutoQC methods are working fine. These were made sometime ago with an earlier version of Skyline. The problem occurs when I try to make a NEW AutoQC config. I opened up one of my working methods, saved the Skyline file using the latest version of Skyline and now it does not work.
The symptoms: When I start the config in AutoQC it does not make an AutoQC.log file. If I make one manually this part then works fine. The file are imported in to Skyline but the Panorama upload fails.
The AutoQC log and Panorama log are attached.
By the way, we still have the issue with AutoQC giving up the ghost every few days when monitoring network drives. It’s annoying, but we just stop the config and start it again...
Thanks,
Peter
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AutoQC.log Panorama.log |
view message |
Skyline 3.7 Support |
(3 responses) |
mdowns2 |
2017-06-14 15:25:15 |
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Hi Panorama Team,
I've just recently updated to Skyline 3.7, and I'm unable to import data to a QC folder on Panorama. (See error messages below.)
Do you know when Skyline 3.7 files will be supported in the QC folders? Or is there some other issue going on?
Thanks,
Melanie Downs
14 Jun 2017 15:17:10,169 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
14 Jun 2017 15:17:10,172 INFO : Starting to import Skyline document from 2017-05-05_P6P_PRM-3_2017-06-14_17-14-51.sky.zip
14 Jun 2017 15:17:10,172 INFO : Expanding 2016_09_07_6ProteinDigest.blib
14 Jun 2017 15:17:10,174 INFO : Expanding 2016_09_07_6ProteinDigest.redundant.blib
14 Jun 2017 15:17:10,186 INFO : Expanding 2017-05-05_P6P_PRM-3.skyd
14 Jun 2017 15:17:10,953 INFO : Expanding 2017-05-05_P6P_PRM-3.sky.view
14 Jun 2017 15:17:10,953 INFO : Expanding 2017-05-05_P6P_PRM-3.sky
14 Jun 2017 15:17:10,973 WARN : The version of this Skyline document is 3.7. This is newer than the highest supported version 3.6
14 Jun 2017 15:17:11,033 INFO : Updating previously imported data for sample file F:\RawDataQE\20161215_P6P.raw in QC folder.
14 Jun 2017 15:17:11,157 INFO : Inserting sp|P02769|ALBU_BOVIN
14 Jun 2017 15:17:12,951 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
14 Jun 2017 15:17:12,952 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - 2017-05-05_P6P_PRM-3_2017-06-14_17-14-51.sky.zip
org.postgresql.util.PSQLException: ERROR: insert or update on table "generalmoleculechrominfo" violates foreign key constraint "fk_gmchrominfo_samplefile"
Detail: Key (samplefileid)=(375166) is not present in table "samplefile".
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view message |
Signal Data Module on PanaramaWeb |
(1 response) |
Jim Collett |
2017-05-08 17:59:50 |
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view message |
Feature Request - Manual Reference Ranges |
(1 response) |
Will Thompson |
2017-04-18 07:03:12 |
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Hi Skyline Panorama Team,
We have been using AutoQC for a few years now (wow time flies!) and we have noticed that the most difficult portion of using the tool in practical 'go/no go' decisions is defining the "guide set" of runs. This is because it is very difficult to find a set of runs which have enough variation for all the metrics, without having too much variation for any of them, to properly capture the reference range. A good example would be retention time; If you perform 5 injections on 5 separate days, while running samples, you might get a good handle on most of the metrics for AutoQC. However if you are using commercial columns the retention time may be extremely tight within that window (say <15-30 seconds variability) which is too narrow to accommodate a column change or larger drifts over time, which may be somewhere in the neighborhood of +/- 1 minute. If we then start using larger sets of runs for guide sets, it is very difficult to find a set of runs over weeks or maybe even a month, which do not contain a single outlier for any of the metrics (and we in theory would not want to have outliers in the 'guide set'). Additionally, some metrics (such as mass accuracy) would make sense to have an 'absolute' cutoff window as opposed to a guide set in any case; for instance, we want all ions to have standard deviation of +/- 1.5 ppm. Allowing the user to utilize historical data to manually set a range for each metric may be more time-consuming for the user to set up, but it would perhaps lead to more accurate go/no go decisions. Another (slightly less appealing) option might be to still use the software to establish a 'guide set', but allow the user to exclude specific runs from specific individual metrics.
Thanks
Will
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view message |
No upload to Panorama from AutoQC |
(6 responses) |
michael plank |
2017-04-12 00:30:08 |
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Hi all,
I`m trying to use AutoQC, but the data do not end up on Panorama. I`m wondering if you might have a look at my settings if I`m getting anything wrong: Screenshots attached.
I set the 'Expected acquisition duration' short, as the files are not written to the folder by the instrument, but I copy-paste them there.
AutoQC says "running", already for several hours on this configuration.
Panorama says "
20170410_RapMock2nd_1
No sample files imported"
I`m also attaching a copy of today`s log entries.
Thanks a lot for your help.
Michael
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sc1.png sc2.png 20170411_todaysLog.txt |
view message |
log file does not exist |
(5 responses) |
n wildburger |
2017-04-09 18:30:51 |
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Hi
I keep getting an error message "log file does not exist" when ever I try to start AutoQC after building a configuration.
I have never seen this error before, and the is not the first time I have installed AutoQC on a system before granted this is an older computer.
Thanks,
Norelle
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view message |