admix assoc --pfile ./BugImputed --pheno ./BugImputed.pheon --pheno-col DISEASE --method ATT,TRACTOR,SNP1 --out AssocTest21 --family binary
2022-01-13 15:15.37 [info     ] Received parameters:
assoc
  --pfile=./BugImputed
  --pheno=./BugImputed.pheon
  --pheno_col=DISEASE
  --out=AssocTest21
  --covar=None
  --method=('ATT', 'TRACTOR', 'SNP1')
  --family=binary
  --fast=True
2022-01-13 15:15.37 [info     ] admix.Dataset: read local ancestry from ./BugImputed.lanc
2022-01-13 15:15.37 [info     ] admix.Dataset: `n_anc` is not provided, infered n_anc from the first 1,000 SNPs is 3. If this is not correct, provide `n_anc` when constructing admix.Dataset
2022-01-13 15:15.37 [info     ] 9344 SNPs and 1480 individuals are loaded
2022-01-13 15:15.37 [info     ] No covariates are loaded
2022-01-13 15:15.37 [info     ] 9344 SNPs and 1480 individuals left after filtering for missing phenotype, or completely missing covariate
2022-01-13 15:15.37 [info     ] Performing association analysis with method ATT
admix.assoc.marginal:  40%|███████████████████████████████████████████████████████████████████████▌                                                                                                           | 4/10 [00:02<00:03,  1.58it/s]
Traceback (most recent call last):
  File "/home/peixott/.local/bin/admix", line 33, in <module>
    sys.exit(load_entry_point('admix-kit', 'console_scripts', 'admix')())
  File "/mnt/beegfs/peixott/admix-kit/admix/cli.py", line 542, in cli
    fire.Fire()
  File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/mnt/beegfs/peixott/admix-kit/admix/cli.py", line 526, in assoc
    dict_rls[m] = admix.assoc.marginal(
  File "/mnt/beegfs/peixott/admix-kit/admix/assoc/__init__.py", line 333, in marginal
    _block_test(
  File "/mnt/beegfs/peixott/admix-kit/admix/assoc/__init__.py", line 71, in _block_test
    var = var.compute()
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/base.py", line 288, in compute
    (result,) = compute(self, traverse=False, **kwargs)
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/base.py", line 571, in compute
    results = schedule(dsk, keys, **kwargs)
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/threaded.py", line 79, in get
    results = get_async(
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 507, in get_async
    raise_exception(exc, tb)
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 315, in reraise
    raise exc
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 220, in execute_task
    result = _execute_task(task, data)
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in <genexpr>
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in <genexpr>
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in <genexpr>
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task
    return func(*(_execute_task(a, cache) for a in args))
  File "/home/peixott/.local/lib/python3.8/site-packages/dask/utils.py", line 37, in apply
    return func(*args, **kwargs)
  File "/home/peixott/.local/lib/python3.8/site-packages/dapgen/_read.py", line 350, in _read_pgen_chunk
    pgen.read_alleles_range(snp_start, snp_stop, geno)
  File "pgenlib.pyx", line 894, in pgenlib.PgenReader.read_alleles_range
  File "pgenlib.pyx", line 922, in pgenlib.PgenReader.read_alleles_range
RuntimeError: variant_idx 4532 read_alleles_range() error 6