Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Uncaught exception in find_exons_in_gene
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1128, in find_exons_worker
    rnaseq_reads, cage_reads, polya_reads )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 1046, in find_exons_in_gene
    gene, rnaseq_reads, cage_reads, polya_reads, ref_elements )
  File "build/bdist.linux-x86_64/egg/grit/find_elements.py", line 650, in build_splice_graph_and_binned_reads_in_gene
    peak_cov,
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 199, in __init__
    type=type)
  File "build/bdist.linux-x86_64/egg/grit/genes.py", line 161, in __init__
    assert stop - start >= 0
AssertionError
Loading None.elements.bed
Building Transcripts
91677: Skipping GENE_2: list indices must be integers, not numpy.float64
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/estimate_transcript_expression.py", line 564, in build_design_matrices_worker
    config.MAX_NUM_TRANSCRIPTS_TO_QUANTIFY)
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 1060, in __init__
    self._build_gene_bnd_arrays(gene, five_p_reads, 'five_p_reads')
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 937, in _build_gene_bnd_arrays
    expected_cnts, observed_cnts, normalize=True )
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 537, in build_expected_and_observed_arrays
    expected_cnts = [transcript_cnts[t] for t in transcripts]
TypeError: list indices must be integers, not numpy.float64
91677: Skipping GENE_3: list indices must be integers, not numpy.float64
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/estimate_transcript_expression.py", line 564, in build_design_matrices_worker
    config.MAX_NUM_TRANSCRIPTS_TO_QUANTIFY)
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 1060, in __init__
    self._build_gene_bnd_arrays(gene, five_p_reads, 'five_p_reads')
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 937, in _build_gene_bnd_arrays
    expected_cnts, observed_cnts, normalize=True )
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 537, in build_expected_and_observed_arrays
    expected_cnts = [transcript_cnts[t] for t in transcripts]
TypeError: list indices must be integers, not numpy.float64
91677: Skipping GENE_4: list indices must be integers, not numpy.float64
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/estimate_transcript_expression.py", line 564, in build_design_matrices_worker
    config.MAX_NUM_TRANSCRIPTS_TO_QUANTIFY)
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 1060, in __init__
    self._build_gene_bnd_arrays(gene, five_p_reads, 'five_p_reads')
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 937, in _build_gene_bnd_arrays
    expected_cnts, observed_cnts, normalize=True )
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 537, in build_expected_and_observed_arrays
    expected_cnts = [transcript_cnts[t] for t in transcripts]
TypeError: list indices must be integers, not numpy.float64
91677: Skipping GENE_1: list indices must be integers, not numpy.float64
Traceback (most recent call last):
  File "build/bdist.linux-x86_64/egg/grit/estimate_transcript_expression.py", line 564, in build_design_matrices_worker
    config.MAX_NUM_TRANSCRIPTS_TO_QUANTIFY)
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 1060, in __init__
    self._build_gene_bnd_arrays(gene, five_p_reads, 'five_p_reads')
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 937, in _build_gene_bnd_arrays
    expected_cnts, observed_cnts, normalize=True )
  File "build/bdist.linux-x86_64/egg/grit/f_matrix.py", line 537, in build_expected_and_observed_arrays
    expected_cnts = [transcript_cnts[t] for t in transcripts]
TypeError: list indices must be integers, not numpy.float64
Read counts: (0, 0, 0)