What does exit status 16 mean?

Germline deep variant 0.8.0. I have verified that the input mapping, the bed file, and the ref genome are all based on the same reference. The same script was used for several other samples and they completed without errors.

I1030 18:44:39.325231 140247813654272 make_examples.py:1164] Writing MakeExamplesRunInfo to /tmp/deepvariant_tmp_output/make_examples.tfrecord-00063-of-00064.gz.run_info.pbtxt
I1030 18:44:39.367234 140247813654272 make_examples.py:1167] Found 484 candidate variants
I1030 18:44:39.367513 140247813654272 make_examples.py:1168] Created 496 examples

real	5m38.670s
user	85m59.188s
sys	1m53.684s
Traceback (most recent call last):
  File "/opt/deepvariant/bin/run_deepvariant.py", line 235, in <module>
    app.run(main)
  File "/usr/local/lib/python2.7/dist-packages/absl/app.py", line 300, in run
    _run_main(main, args)
  File "/usr/local/lib/python2.7/dist-packages/absl/app.py", line 251, in _run_main
    sys.exit(main(argv))
  File "/opt/deepvariant/bin/run_deepvariant.py", line 215, in main
    subprocess.check_call(command, shell=True, executable='/bin/bash')
  File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'time seq 0 63 | parallel -k --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "ref.fa" --reads "input.bam" --examples "/tmp/deepvariant_tmp_output/[e-mail]" --regions "regions.bed" --gvcf "/tmp/deepvariant_tmp_output/[e-mail]" --task {}' returned non-zero exit status 16

[pichuan]

Hi @bopohdr Thank you, the log is helpful. From the error, specifically this line:

ValueError: Failed precondition: Cannot query without an index

It looks like maybe your BAM file doesn’t have a corresponding *.bai file. Can you double check that your input BAM file has a correct *.bai file associated with it? Usually, if you have a BAM file named foo.bam, there should be a corresponding foo.bam.bai or foo.bai in the same directory.

If it doesn’t exist, please run: samtools index foo.bam to generate an index file before you proceed.

Let me know if this resolves your issue. Thank you!

[pichuan]

Hi @sclan to give you an update, I made an internal fix to make sure run_deepvariant.py can output more clear errors when they occur. The new code is not on GitHub yet, but will come out in the next release.

Specifically, I changed the main function to be:

def main(_):
  check_or_create_intermediate_results_dir(FLAGS.intermediate_results_dir)
  check_flags()

  commands = create_all_commands()
  for command in commands:
    print('\n***** Running the command:*****\n{}\n'.format(command))
    try:
      subprocess.check_call(command, shell=True, executable='/bin/bash')
    except subprocess.CalledProcessError as e:
      logging.info(e.output)
      raise