Exit Status 140

[shyama-mama]

Hi, I've exported the Docker pkrusche/hap.py to a singularity image to run Hap.py The Hap.py command that run in the singularity image is as follows: /opt/hap.py/bin/hap.py ${TRUTH} ${QUERY} -f ${BED} -o ${PREFIX} -r ${REF}

The command runs and exits 140 without any error message. This was the only output by the command.

 2020-01-20 17:21:22,386 WARNING  No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
  2020-01-20 17:21:22,391 WARNING  No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
  [W] overlapping records at 1:5939836 for sample 0
  [W] Variants that overlap on the reference allele: 1187
  [I] Total VCF records:         494941218
  [I] Non-reference VCF records: 5009070
  [I] Total VCF records:         155035
  [I] Non-reference VCF records: 736

The runinfo.json file can be downloaded from here

Thanks.