Can you please sort out the problem with importing Dawn & Patrick's MiSeq49 run #183 into Labkey. We really need to make this work on a regular basis instead of fighting with it every other time we do a run.
pipeline_user log seems fine : Logging in on the usual 10 minute cycle.
Crontab : looking good, no changes in either script or in the crontab entries.
Scripts worked fine when initiated manually , Gave error in the labkey data processing pipeline :
org.labkey.api.pipeline.PipelineJobException: The sample Id was not an integer
Other possible reasons : I will keep observing the scripts for the current run. Hopefully the reason behind the failure of scripts to process last run might get clear.
The scripts worked automatically and imported the next run(183) in couple of hours. Seems like the problem was run specific.
resolve as Fixed
The Problem was the extra blank line at the end of the samplesheet.