GermlineCNVCaller, some samples do not have read depth metadata

GATK4.1.0.0, linux server, bash

Hi, I'm testing the following commands:

  ${GATK4} --java-options "${javaOpt}" DetermineGermlineContigPloidy \
  -L ${fol7}/"${INTERVAL}.preprocessed.interval_list" \
  --interval-merging-rule "OVERLAPPING_ONLY" \
  ${INPUT.hdf5} \
  --contig-ploidy-priors ${fol8}/ContigPloidyPriors.tsv \
  -O ${fol8}/"Karyo"/ \
  --output-prefix "Karyo_cohort" \
  --verbosity "DEBUG" \
  --tmp-dir ${tmp}/

 ${GATK4} --java-options "${javaOpt}" GermlineCNVCaller \
 --run-mode COHORT \
 -L ${fol7}/"${INTERVAL}.preprocessed.interval_list" \
 --interval-merging-rule "OVERLAPPING_ONLY" \
  --contig-ploidy-calls ${fol8}/"Karyo"/ \
 ${INPUT.hdf5} \
 --output ${fol8}/"germCNV"/ \
 --output-prefix "germCNV_cohort" \
 --verbosity "DEBUG" \
 --tmp-dir ${tmp}/

In both tools (DetermineGermlineContigPloidy, GermlineCNVCaller) I used the same interval and the same input files... I can not figure out why in the second command "GermlineCNVCaller" I have the following error: "Some samples do not have read depth metadata"

Part of the logs:

  Traceback (most recent call last):
    File "/home/manolis/GATK4/tmp/cohort_denoising_calling.6605166682471840218.py", line 133, in <module>
      n_st, sample_names, sample_metadata_collection)
    File "/share/apps/bio/miniconda2/envs/gatk4100/lib/python3.6/site-packages/gcnvkernel/models/model_denoising_calling.py", line 379, in __init__
      sample_metadata_collection, sample_names, self.contig_list)
    File "/share/apps/bio/miniconda2/envs/gatk4100/lib/python3.6/site-packages/gcnvkernel/models/model_denoising_calling.py", line 618, in _get_baseline_
  copy_number_and_read_depth
      "Some samples do not have read depth metadata"
  AssertionError: Some samples do not have read depth metadata
  17:51:21.529 DEBUG ScriptExecutor - Result: 1
  17:51:21.531 INFO  GermlineCNVCaller - Shutting down engine
  [March 1, 2019 5:51:21 PM CET] org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller done. Elapsed time: 0.77 minutes.
  Runtime.totalMemory()=3591372800
  org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
  python exited with 1
  Command Line: python ...
  ....
          at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
          at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
          at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)

...

Many thanks for any help!