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[May 20 17:24:15] Running TensorQTL: cis-QTL mapping
  * using GPU (Tesla V100-SXM2-32GB)
  * reading phenotypes (expression_data.filtered.bed.gz)
  * reading covariates (franke_covariates.txt)
cis-QTL mapping: empirical p-values for phenotypes
  * 44 samples
  * 13115 phenotypes
  * 2 covariates
  * 3954267 variants
  * checking phenotypes: 1000/13115  * checking phenotypes: 2000/13115  * checking phenotypes: 3000/13115  * checking phenotypes: 4000/13115  * checking phenotypes: 5000/13115  * checking phenotypes: 6000/13115  * checking phenotypes: 7000/13115  * checking phenotypes: 8000/13115  * checking phenotypes: 9000/13115  * checking phenotypes: 10000/13115  * checking phenotypes: 11000/13115  * checking phenotypes: 12000/13115  * checking phenotypes: 13000/13115  * checking phenotypes: 13115/13115
    ** dropping 507 phenotypes without variants in cis-window
  * computing permutations
    processing phenotype 1/12608    processing phenotype 2/12608    processing phenotype 3/12608    processing phenotype 4/12608    processing phenotype 5/12608    processing phenotype 6/12608    processing phenotype 7/12608    processing phenotype 8/12608    processing phenotype 9/12608    processing phenotype 10/12608    processing phenotype 11/12608    processing phenotype 12/12608    processing phenotype 13/12608    processing phenotype 14/12608    processing phenotype 15/12608    processing phenotype 16/12608    processing phenotype 17/12608    processing phenotype 18/12608    processing phenotype 19/12608    processing phenotype 20/12608    processing phenotype 21/12608    processing phenotype 22/12608    processing phenotype 23/12608    processing phenotype 24/12608    processing phenotype 25/12608    processing phenotype 26/12608    processing phenotype 27/12608    processing phenotype 28/12608    processing phenotype 29/12608    processing 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scipy.optimize.minimize)
    processing phenotype 686/12608    processing phenotype 687/12608    processing phenotype 688/12608    processing phenotype 689/12608    processing phenotype 690/12608    processing phenotype 691/12608    processing phenotype 692/12608    processing phenotype 693/12608    processing phenotype 694/12608    processing phenotype 695/12608    processing phenotype 696/12608    processing phenotype 697/12608    processing phenotype 698/12608    processing phenotype 699/12608    processing phenotype 700/12608    processing phenotype 701/12608    processing phenotype 702/12608    processing phenotype 703/12608    processing phenotype 704/12608    processing phenotype 705/12608    processing phenotype 706/12608    processing phenotype 707/12608    processing phenotype 708/12608    processing phenotype 709/12608    processing phenotype 710/12608    processing phenotype 711/12608    processing phenotype 712/12608    processing phenotype 713/12608    processing phenotype 714/12608    processing phenotype 715/12608    processing phenotype 716/12608    processing phenotype 717/12608    processing phenotype 718/12608    processing phenotype 719/12608    processing phenotype 720/12608    processing phenotype 721/12608    processing phenotype 722/12608    processing phenotype 723/12608    processing phenotype 724/12608    processing phenotype 725/12608    processing phenotype 726/12608    processing phenotype 727/12608    processing phenotype 728/12608    processing phenotype 729/12608    processing phenotype 730/12608    processing phenotype 731/12608    processing phenotype 732/12608    processing phenotype 733/12608    processing phenotype 734/12608    processing phenotype 735/12608    processing phenotype 736/12608    processing phenotype 737/12608    processing phenotype 738/12608    processing phenotype 739/12608    processing phenotype 740/12608    processing phenotype 741/12608    processing phenotype 742/12608    processing phenotype 743/12608    processing phenotype 744/12608    processing phenotype 745/12608    processing phenotype 746/12608    processing phenotype 747/12608    processing phenotype 748/12608    processing phenotype 749/12608WARNING: scipy.optimize.newton failed to converge (running scipy.optimize.minimize)
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/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/tensorqtl/core.py:217: RuntimeWarning: invalid value encountered in sqrt
  return 2*stats.t.cdf(-np.abs(np.sqrt(tstat2)), dof)
/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in greater
  return (a < x) & (x < b)
/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in less
  return (a < x) & (x < b)
/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/scipy/stats/_distn_infrastructure.py:1827: RuntimeWarning: invalid value encountered in greater_equal
  cond2 = (x >= np.asarray(_b)) & cond0
Traceback (most recent call last):
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/tensorqtl/__main__.py", line 2, in <module>
    tensorqtl.main()
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/tensorqtl/tensorqtl.py", line 109, in main
    logger=logger, seed=args.seed, verbose=True)
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/tensorqtl/cis.py", line 460, in map_cis
    res = calculate_cis_permutations(genotypes_t, phenotype_t, residualizer, permutation_ix_t)
  File "/lustre/scratch118/humgen/resources/conda_envs/tensorqtl/lib/python3.5/site-packages/tensorqtl/cis.py", line 64, in calculate_cis_permutations
    return r_nominal_t[ix], std_ratio_t[ix], ix, r2_perm_t, genotypes_t[ix]
IndexError: too many indices for tensor of dimension 0


Exited with exit code 1.

Resource usage summary:

    CPU time :                                   744.00 sec.
    Max Memory :                                 3362 MB
    Average Memory :                             3121.70 MB
    Total Requested Memory :                     56320.00 MB
    Delta Memory :                               52958.00 MB
    Max Swap :                                   -
    Max Processes :                              16
    Max Threads :                                87
    Run time :                                   765 sec.
    Turnaround time :                            765 sec.

The output (if any) is above this job summary.