Skyline 3.7 Support

Skyline 3.7 Support mdowns2  2017-06-14 15:25:15
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?

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
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
14 Jun 2017 15:17:10,953 INFO : Expanding
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 -
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".
vsharma responded:  2017-06-14 15:59:23
Hi Melanie,

This error is not due to Skyline 3.7, even though you see the warning in the log! I will have to take a look at your document to figure this out. Just want to confirm that the QC folder where you are seeing this error is:

vsharma responded:  2017-06-14 16:27:42
Hi Melanie,

You are getting this error because you have at least one raw file (F:\RawDataQE\20161215_P6P.raw) imported twice as different replicate names (20161215_70-70_2e5_4.0kV and 20161215_P6P) in your Skyline document. If you remove one of them, assuming there are no other such duplicates, your should be able to import the document into Panorama.

mdowns2 responded:  2017-06-15 11:20:27
Hi Vagisha,

Thanks for the quick response! I removed the duplicate and things are working well now.