Usage example; rescale_chroms parameter input

[lokeyCEU]

Hello,

I am trying to get PhyloP estimates for my bird species of interest using the Bird10k 363way.hal resource. I have the 363way.hal (from the UCSC cactus site) and am attempting to run the neutral-model-estimator as described in the Feng et al. paper. I run the code, as described in the README

  luigi --module neutral_model_estimator GenerateNeutralModel \
        --num-bases 30000 --neutral-data ancestral_repeats \
        --work-dir /workdir/${USER}/${newdir}/avian_ancestral_repeats_model_rev \
        --HalPhyloPTrain-model-type REV --hal-file 363-avian-2020.hal \
        --genome root --no-single-copy --local-scheduler \
        --GenerateAncestralRepeatsBed-rm-species 'aves'

But I get this error;

    ERROR: Uncaught exception in luigi
    Traceback (most recent call last):
    File "/usr/lib/python2.7/site-packages/luigi/retcodes.py", line 74, in run_with_retcodes
        worker = luigi.interface._run(argv)['worker']
    File "/usr/lib/python2.7/site-packages/luigi/interface.py", line 237, in _run
        return _schedule_and_run([cp.get_task_obj()], worker_scheduler_factory)
    File "/usr/lib/python2.7/site-packages/luigi/cmdline_parser.py", line 116, in get_task_obj
        return self._get_task_cls()(**self._get_task_kwargs())
    File "/usr/lib/python2.7/site-packages/luigi/task_register.py", line 88, in __call__
        param_values = cls.get_param_values(params, args, kwargs)
    File "/usr/lib/python2.7/site-packages/luigi/task.py", line 360, in get_param_values
        raise parameter.MissingParameterException("%s: requires the '%s' parameter to be set" % (exc_desc, param_name))
    MissingParameterException: GenerateNeutralModel[args=(), kwargs={'hal_file': '363-avian-2020.hal', 'work_dir': '/workdir/mgl77/phast363.347830/avian_ancestral_repeats_model_rev', 'no_single_copy': True, 'neutral_data': 'ancestral_repeats', 'genome': 'root', 'num_bases': 30000}]: requires the 'rescale_chroms' parameter to be set

Looking through init_.py and rescale.py I understand the rescale_chroms option calls RescaleNeutralModel and expects an input with sets of chromosomes with a name for each set (read as a python dictionary). I'm not sure if these dictionaries are supposed to be species and their chromosomes, chromosome groups and the individual chromosomes, or? I presume it's expecting chromosome sets for chromosomes of a single species (e.g. macro vs micro for chickens). Is that correct? And if so what should the format of the file be?

I'm also curious how this relates to the rescaling in the README, where it was suggested to use halLiftover and phylofit.