collate function not working

[moks-micro]

Hi Jody,

The collate function for ntm-profiler doesn't work when one or more of the datasets dont have a match for the 'closest species' and I have had manually delete individual datasets for it to work. Is there a way to get the collate function without have to exclude individual datasets ? Thanks in advance :)

ntm-profiler error report

• OS: linux
• ntm-profiler version: 0.2.2
• pathogen-profiler version: 2.0.4
• Program call:

{'no_clean': False, 'outfile': 'ntmprofiler.collate.txt', 'samples': None, 'dir': '.', 'suffix': '.results.json', 'format': 'txt', 'temp': '.', 'func': <function main_collate at 0x7f3655cc8ee0>, 'software_name': 'ntm-profiler', 'tmp_prefix': '51715690-f70f-4364-b281-3e36e1e9fbbe', 'files_prefix': './51715690-f70f-4364-b281-3e36e1e9fbbe'}

Traceback:

  File "/home/simone/miniconda3/envs/ntm-profiler/bin/ntm-profiler", line 355, in <module>
    args.func(args)
  File "/home/simone/miniconda3/envs/ntm-profiler/bin/ntm-profiler", line 172, in main_collate
    ntmp.collate(args)
  File "/home/simone/miniconda3/envs/ntm-profiler/lib/python3.8/site-packages/ntm_profiler/output.py", line 209, in collate
    closest_seq[s] = "|".join(pp.stringify(data["mash_closest_species"]["prediction"][0].values()))

Value:

list index out of range```