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?
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"?
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 (188.8.131.5292. 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.
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.
Problem Event Name: CLR20r3
Problem Signature 01: Skyline.exe
Problem Signature 02: 184.108.40.206
Problem Signature 03: 593f676f
Problem Signature 04: Skyline
Problem Signature 05: 220.127.116.11
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
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 18.104.22.16834, and Skyline version is 22.214.171.12417 64 bit.
Please advise on how to get automatic uploading working again.
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.
The QC plots that are displayed do not have the same x-axis (replicates). The DGL... peptides shows several datapoints for the the date 2017-09-03. For the ECC... there is several injections missing. How is this possible? If I co-plot all peptide it gets even more visible (see attachment).
Interestingly, all peptides that are missing belong to the same protein group.
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?
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.
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
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 126.96.36.19926 and Skyline is V188.8.131.5240, 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...
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?
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".
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.
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 "
No sample files imported"
We have an issue with the most recent results not showing up in Panorama folder /Duke Proteomics Core/QC. Since 3/1, the AutoQC Loader on the PC loads the data into Skyline and then the log shows that it is pushed to Panorama, but the data never shows up in the Levy-Jennings or other plots. The data HAS been loaded to panorama because I can see them listed in the "RUNS" tab. Please take a look and let me know what you find. I have given admin access to that folder to firstname.lastname@example.org.
We have been uploading DDA runs to Panorama (through AutoQC) for several months now without any major issues. We have used the latest Skyline-daily builds (currently 184.108.40.20656). Since about 3/9/2017, we have been getting errors at the end of the skyline file upload both when using AutoQC, or when trying to manually upload the files from within the Skyline application. I have attached the logs for the AutoQC (v220.127.116.1105) and the Skyline applications, and an example sky.zip file. We can't remember exactly whether this error coincided with our latest upgrade of Skyline-daily to the most recent build, but it might be related.
we have AutoQC setup to monitor several MS with a number of different configuration files. All of them work *most* of the time. We have noticed that after a few days (we are still working out how long), AutoQC stops working for some of the configurations. If you stop the individual configuration (as opposed to the AutoQC application) and restart it, the files are successfully processed. It is possible ALL the configurations are doing this, it’s just that we haven’t noticed as those particular configurations aren’t supposed to be processing any files at this point in time. As such, it may be a global issue, or a local issue, we aren't 100% sure as yet.
We have other software running on the same PC doing a very similar thing (syncing files) and it is not experiencing any issues, so we don’t think it’s related to computer sleep issues (the PC is set to stay wake all the time, ditto the HDD).
Currently, I am using AutoQC on our Fusion so we can monitor instrument performance with the PRTC mix from Thermo.
Auto QC runs fine, but no files or results are on our folder on Panorama.
Attached is the Skyline template for of PRTC peptides we monitor, which to me looks fine. However, the instrument method used for the PRTC standard is a targeted MS2, meaning there is no MS1. I think this is why the AutoQC fails since a lot of the metrics are from the MS1 (correct me if I'm wrong). And since there is no MS1 my database search with PEAKS fails so I cannot create a spectral library.
I am having an issue with using the Publish to Panorama option in Skyline to publish to our PanoramaWeb project. When I attempt the upload I can see the appropriate project and subfolders, but I receive the following 404 error message:"The remote server returned an error: (404) Not Found." I have attached a screen grab with details.
I keep getting the error message below. Sometimes it appears as below but I have also had a pop-up error that causes the AutoQC Loader app to quit altogether, which is problematic since I have other configurations actively importing files when the Loader quits. I am trying to import a .raw file. I have made sure that it is newly added to the "watch" folder, that it is not in the skyline document, and that it is not already uploaded as a "sample file" on Panorama. Now, AutoQC Loader just seems to be stuck. It won't recognize any new raw files that I drop into the "watch" folder for this particular configuration. I have attached the log file showing the errors.
An exception occurred while importing the file.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
at AutoQC.AutoQcLogger.WriteToFile(String message)
at AutoQC.AutoQcLogger.LogError(String message)
at AutoQC.AutoQcLogger.LogException(Exception ex)
at AutoQC.ConfigRunner.RunConfiguration(Object sender, DoWorkEventArgs e)
at System.ComponentModel.BackgroundWorker.OnDoWork(DoWorkEventArgs e)
at System.ComponentModel.BackgroundWorker.WorkerThreadStart(Object argument)
Is mass accuracy data stored in skyline or controlled by a setting in the skyline document? I have 4 AutoQC folders and can see mass accuracy data for the runs in all of them except for one ("AutoQC_BSA_Fus") (see attached screen shot). I have compared the settings in all four skyline documents and cannot seem to find anything that is different in the file associated with the folder in which runs have no mass accuracy data.
I am getting this error whenever AutoQC Loader tries to import my skyline document to Panorama. I am using Skyline version 18.104.22.16819, 64-bit. Any idea what is going on?
30 Sep 2016 07:14:18,818 INFO : Starting to import Skyline document from Weekly_Yeast_QEx_2016-09-30_10-13-58.sky.zip
30 Sep 2016 07:14:18,818 INFO : Expanding Weekly_Yeast_QEx.skyd
30 Sep 2016 07:14:18,859 INFO : Expanding Weekly_Yeast_QEx.sky.view
30 Sep 2016 07:14:18,860 INFO : Expanding Weekly_Yeast_QEx.sky
30 Sep 2016 07:14:18,861 WARN : The version of this Skyline document is 3.5. This is newer than the highest supported version 2.62
30 Sep 2016 07:14:19,525 INFO : Inserting peptides1
30 Sep 2016 07:14:19,570 ERROR: Skyline document import failed
java.lang.IllegalStateException: 'test' library not found in settings.
Hi, I'm wondering where I can find descriptions or documentation on APIs or programmatic access to Skyline data in Panorama. This PDF suggests that APIs exist (page 23) but I can't find any more info anywhere. Thanks Gabe
I get the following error message when I start runnign AutoQC:
ERROR: Error getting status of file D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw
ERROR: Exception details can be found in the AutoQC log in C:\Users\Q1\Documents\PRM
Adding D:\Data\BSA\20160726_UC_ColID_163_CKF_BSA_50fmol_test2.raw to re-import queue.
ive set up a skyline file with MRM transitions for 8 small molecules and the data is successfully imported by the autoqc daemon and uploaded to the panorama server. Unfortunaterly, panorama doesnt display the data and gives an error message...
There were no records found. The date filter applied may be too restrictive.
We have a skyline file containing discovery data (DDA runs of which we build a spectral lib with the dat files from mascot) and no target data. When importing into panorama, it puts this skyline file in the "targeted MS runs" section. Is there a way to annotate that this is a discovery experiment, present in skyline?
We wanted to import our skyline files on our subfolder on Panorama, but we managed to import only 2 out of 10.
All the rest of the files throw the same error (see screenshot): java.lang.IllegalArgumentException: No enum constant org.labkey.targetedms.parser.DataSettings.AnnotationType.-1
I imported a skyline document to Panorama that I zipped via the "share"-> "minimal" option. In my skyline document I have several replicates with ms/ms information. In the Panorama view only one ms/ms is displayed for a given peptide. How can I see which replicate (and wich r.t. if there are several ms/ms for one replicate) it belongs to?
Is it possile to choose which ms/ms will be displayed in Panorama before zipping the file? Or can I display the ms/ms information for all replicates?
So I duplicated my skyline file and removed the results and re saved it. I wanted to add a few more peptides to my QC. When I run autoQC again (pointing to the new skyline file and uploading to a new sub directory on Panorama) I get "An Item with the same key has already been added" and then an Error failed importing. Any ideas on how to fix this?
Hi, i'm trying to set up autoqc and publish to panaroma, but I can't figure out my project name to put in the "Folder on Panorama" box. I think my project has spaces in it which may be causing the problem
Hi, I've been uploading files into Panorama without any issues, except that there are two files that give me this error: Error renaming temporary zip file: A remote server returned an error: (412) Precondition Failed. Any idea of how to fix this would be great! Thanks.
I am just getting some errors while trying to upload a file to Panorama from Skyline. I have tried to import the file using both manual upload of a zipped Skyline file and also uploading from Skyline directly to Panorama.
I am following the tutorial for publishing data in Panorama. When doing: "If you use a fake email
address you can set the password for the account by clicking on a link to the email message that gets
generated for the new user.", the link to the message does not appear, instead I have:
"System membership status for new group members:
email@example.com added as a new user to the system and emailed successfully."
My collaborator just upload our MRM data to Panorama and I was able to view the result in the morning. After tried to download the Zip file and failed many times, I cannot see my result anymore ( I can still see the folder and the file but cannot see the chromatogram or other parts). Once I click the peptide, the panoroma stop working. I tried to download the zip file but always stopped after very long waiting. The web browser indicated some server error. Could you please give me some suggestions? Very appreciate.
I have a question regarding the Targeted MS Runs webpart in my project. I seem to be unable to remove webparts in a 'Targeted MS' folder. I have duplicate parts but seem to be unable to remove them (I'm admin for the project currently), I don't see the 'x' at top right of part title.