GADO doesn't produce all_samples.txt in some cases

[dennishendriksen]

GADO can exit without an error but fail to produce all_samples.txt file that downstream tools depend on:

gado_process() {
  echo -e -n "all_samples" > gadoProcessInput.tsv
  local -r hpo_ids="HP:0000001"
  for i in $(echo "${hpo_ids}" | sed "s/,/ /g")
  do
      echo -e -n "\t${i}" >> gadoProcessInput.tsv
  done

  local args=()
  args+=("-Djava.io.tmpdir=\"${TMPDIR}\"")
  args+=("-XX:ParallelGCThreads=2")
  args+=("-jar" "/opt/gado/lib/GADO.jar")
  args+=("--mode" "PROCESS")
  args+=("--output" "gadoProcessOutput.tsv")
  args+=("--caseHpo" "gadoProcessInput.tsv")
  args+=("--hpoOntology" "/groups/umcg-gcc/tmp02/vip/main/resources/gado/v1.0.1/hp.obo")
  args+=("--hpoPredictionsInfo" "/groups/umcg-gcc/tmp02/vip/main/resources/gado/v1.0.1/predictions_auc_bonf.txt")

  ${CMD_GADO} java "${args[@]}"
}

gado_prioritize() {
  local args=()
  args+=("-Djava.io.tmpdir=\"${TMPDIR}\"")
  args+=("-XX:ParallelGCThreads=2")
  args+=("-jar" "/opt/gado/lib/GADO.jar")
  args+=("--mode" "PRIORITIZE")
  args+=("--output" "./gado")
  args+=("--caseHpoProcessed" "gadoProcessOutput.tsv")
  args+=("--genes" "/groups/umcg-gcc/tmp02/vip/main/resources/gado/v1.0.1/hpo_prediction_genes.txt")
  args+=("--hpoPredictions" "/groups/umcg-gcc/tmp02/vip/main/resources/gado/v1.0.1/genenetwork_bonf_spiked")

  ${CMD_GADO} java "${args[@]}"
}

gado_process
gado_prioritize

in this example HP:0000001 is used, which isn't a phenotype, but the issue probably occurs for other HPO terms as well.

I would expect GADO to either throw an error that the HPO term is not a valid phenotype or produce an all_samples.txt file containing only a header.