---------
NOC2L-201, NOC2L|PB.8.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(397, 397) and range(245, 245)
---------
---------
PLEKHN1-203, PLEKHN1|PB.9.1
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(839:2490|1174:2825), M(662:839|899:1076), and perhaps more.
---------
---------
UBE2J2-202, UBE2J2|PB.18.20
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(44, 44) and range(44, 44)
---------
---------
PUSL1-201, PUSL1|PB.21.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
FAAP20-202, FAAP20|PB.55.19
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
FAAP20-202, FAAP20|PB.55.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
ICMT-201, ICMT|PB.78.16
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(152, 152) and range(95, 95)
---------
---------
DNAJC11-202, DNAJC11|PB.91.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(235, 235) and range(235, 235)
---------
---------
VAMP3-201, VAMP3|PB.94.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
CTNNBIP1-201, CTNNBIP1|PB.114.1
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(62, 62) and range(62, 62)
---------
---------
FBXO44-202, FBXO44|PB.131.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(131, 131) and range(131, 131)
---------
---------
CLCN6-202, CLCN6|PB.138.13
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(318, 318) and range(290, 290)
---------
---------
MFAP2-202, MFAP2|PB.180.8
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(80, 80) and range(80, 80)
---------
---------
ATP13A2-203, ATP13A2|PB.181.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(0:295|3:298), M(295:3981|343:4029), and perhaps more.
---------
---------
RCC2-201, RCC2|PB.188.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
HP1BP3-201, HP1BP3|PB.214.40
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 295, in from_transcripts
    assert anchor.length - position['anchor'] == other.length - position['other'], f'{position=}, {anchor.length=}, {other.length=}, {anchor=}'
AssertionError: position={'anchor': 3885, 'other': 2700}, anchor.length=3884, other.length=2700, anchor=HP1BP3-201
---------
---------
KDM1A-203, KDM1A|PB.236.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(492, 492) and range(492, 492)
---------
---------
SRSF10-204, SRSF10|PB.254.42
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(56, 56) and range(23, 23)
---------
---------
NUDC-201, NUDC|PB.299.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(469:535|552:618), M(535:652|1459:1576), and perhaps more.
---------
---------
PHACTR4-202, PHACTR4|PB.324.8
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(55, 55) and range(69, 69)
---------
---------
EPB41-201, EPB41|PB.338.8
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 540, in one
    first_value = next(it)
                  ^^^^^^^^
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 553, in from_proteins
    tblock = one(interval.data for interval in intervals if interval.data.category in SEQ_DEL_INS)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 542, in one
    raise (
ValueError: too few items in iterable (expected 1)
---------
---------
SRSF4-201, SRSF4|PB.337.23
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 3386; expected 543
---------
---------
PUM1-201, PUM1|PB.344.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(1038, 1038) and range(567, 567)
---------
---------
S100PBP-202, S100PBP|PB.379.12
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 2066; expected -1077
---------
---------
SH3D21-202, SH3D21|PB.417.3
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(757, 757) and range(0, 0)
---------
---------
YRDC-201, YRDC|PB.426.1
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
YRDC-201, YRDC|PB.426.3
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
TRIT1-201, TRIT1|PB.450.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
TRIT1-201, TRIT1|PB.450.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(105, 105) and range(62, 62)
---------
---------
CTPS1-201, CTPS1|PB.471.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(1523:1579|1445:1501), M(1579:2037|1580:2038), and perhaps more.
---------
---------
HYI-202, HYI|PB.501.3
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(449:564|1613:1728), M(337:449|435:547), and perhaps more.
---------
---------
HYI-202, HYI|PB.501.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(254, 254) and range(248, 248)
---------
---------
HYI-202, HYI|PB.501.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(254, 254) and range(273, 273)
---------
---------
UROD-201, UROD|PB.523.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(288:486|426:624), M(225:288|344:407), and perhaps more.
---------
---------
UROD-201, UROD|PB.523.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(288:486|624:822), M(225:288|322:385), and perhaps more.
---------
---------
GPBP1L1-201, GPBP1L1|PB.536.39
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(295, 295) and range(0, 0)
---------
---------
STIL-203, STIL|PB.554.13
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(871, 871) and range(871, 871)
---------
---------
TUT4-201, TUT4|PB.575.16
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(1246, 1246) and range(1175, 1175)
---------
---------
MYSM1-202, MYSM1|PB.614.1
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(166, 166) and range(122, 122)
---------
---------
MYSM1-202, MYSM1|PB.614.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(166, 166) and range(125, 125)
---------
---------
SSX2IP-201, SSX2IP|PB.698.16
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(405, 405) and range(405, 405)
---------
---------
FNBP1L-201, FNBP1L|PB.743.21
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 2341; expected -1500
---------
---------
DBT-202, DBT|PB.762.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
AMPD2-201, AMPD2|PB.801.10
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(1929:2093|1970:2134), M(1797:1929|1691:1823), and perhaps more.
---------
---------
LRIF1-201, LRIF1|PB.814.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(532, 532) and range(23, 23)
---------
---------
PPM1J-201, PPM1J|PB.834.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
SYT6-209, SYT6|PB.852.27
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 3976; expected -248
---------
---------
TTF2-201, TTF2|PB.872.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(1090, 1090) and range(1090, 1090)
---------
---------
NOTCH2NLB-201, NOTCH2NLB|PB.945.10
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(285:1077|302:1094), M(0:285|9:294), and perhaps more.
---------
---------
SELENBP1-201, SELENBP1|PB.1004.3
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(125:238|283:396), M(238:1720|648:2130), and perhaps more.
---------
---------
DENND4B-201, DENND4B|PB.1036.19
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(4064:4200|217:353), M(4200:4437|554:791), and perhaps more.
---------
---------
JTB-201, JTB|PB.1042.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(68, 68) and range(28, 28)
---------
---------
TPM3-224, TPM3|PB.1043.48
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 218; expected -3423
---------
---------
MTX1-207, MTX1|PB.1080.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(236:492|228:484), M(45:236|0:191), and perhaps more.
---------
---------
FAM189B-202, FAM189B|PB.1078.19
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(888:999|1263:1374), M(831:888|1001:1058), and perhaps more.
---------
---------
GLMP-201, GLMP|PB.1106.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(126, 126) and range(40, 40)
---------
---------
NCSTN-201, NCSTN|PB.1142.13
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(245, 245) and range(64, 64)
---------
---------
NIT1-203, NIT1|PB.1150.1
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
NIT1-203, NIT1|PB.1150.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
NIT1-203, NIT1|PB.1150.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(7, 7)
---------
---------
NIT1-203, NIT1|PB.1150.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(7, 7)
---------
---------
PPOX-201, PPOX|PB.1156.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(74, 74) and range(74, 74)
---------
---------
DUSP12-201, DUSP12|PB.1163.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
POU2F1-204, POU2F1|PB.1186.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(271, 271) and range(58, 58)
---------
---------
MPZL1-201, MPZL1|PB.1192.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(158, 158) and range(31, 31)
---------
---------
RABGAP1L-201, RABGAP1L|PB.1235.17
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to 5673; expected 1387
---------
---------
TOR1AIP2-201, TOR1AIP2|PB.1259.17
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 301, in from_transcripts
    return cls(anchor, other, events, anchor_events, anchor_blocks, other_events, other_blocks, event_to_block, block_to_events)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.TranscriptAlignment>", line 34, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 174, in __attrs_post_init__
    raise ValueError(f'TranscriptEvent lengths add up to {total_delta_nt}; expected {tx_length_diff}')
ValueError: TranscriptEvent lengths add up to -3485; expected -5695
---------
---------
CEP350-202, CEP350|PB.1256.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 540, in one
    first_value = next(it)
                  ^^^^^^^^
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 553, in from_proteins
    tblock = one(interval.data for interval in intervals if interval.data.category in SEQ_DEL_INS)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 542, in one
    raise (
ValueError: too few items in iterable (expected 1)
---------
---------
GLUL-201, GLUL|PB.1266.26
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(1500:3521|824:2845), M(1372:1500|493:621), and perhaps more.
---------
---------
ARPC5-202, ARPC5|PB.1276.3
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(48, 48) and range(48, 48)
---------
---------
ODR4-201, ODR4|PB.1294.9
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(333, 333) and range(333, 333)
---------
---------
PIK3C2B-202, PIK3C2B|PB.1365.4
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(1016, 1016) and range(1016, 1016)
---------
---------
DSTYK-202, DSTYK|PB.1373.8
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(746, 746) and range(746, 746)
---------
---------
RCOR3-203, RCOR3|PB.1410.14
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(439, 439) and range(381, 381)
---------
---------
TATDN3-202, TATDN3|PB.1429.6
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
C1orf35-201, C1orf35|PB.1513.7
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(389:472|479:562), M(472:545|657:730), and perhaps more.
---------
---------
RBM34-201, RBM34|PB.1565.5
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(17, 17) and range(17, 17)
---------
---------
CATSPERE-203, CATSPERE|PB.1595.2
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(143, 143) and range(20, 20)
---------
---------
HNRNPU-205, HNRNPU|PB.1600.51
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_wtc11/cblock-tables/cblocks-chr1.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(618, 618) and range(618, 618)
---------
