DetermineGermlineContigPloidy - Badly formed genome unclippedLoc

[stefandiederich]

Dear Sir or Madame,

I use GATK 4.6.2.0 Docker Container and got the following error message during use of DetermineGermlineContigPloidy:

A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "/media/Data/AnnotationDBs/CNV/ExomV8Cre4_P4/ExomV8Cre4_P4/ExomV8Cre4_P4.filterd.neu.interval_list" is not valid for this input.

This interval file was produced the steps of

1. PreprocessIntervals
2. AnnotateIntervals
3. FilterIntervals

Can you give me an Idea of what is going wrong here?

Bests Stefan