No files are synced when you start the NGI pipeline with the -k flag.

[Smeds]

A common failure when running the NGI pipeline is that recalibration failes and then you would like restart the analysis at this step. At this stage you have already generated the alignment and some qc, which have taken a few days.
When the -k flag is used, the NGI pipeline tries setup a rsync commando to sync the already generated files, but no files are synced.

Please have a look at this folder /proj/a2015179/nobackup/patriksm/ngiPipelineFailToSync/ on nestor. Here you can find a sbatch file where the NGI pipeline tries to sync the data without success and a file with the actual files on the hard drive (when the analysis has started).