uio-bmi / graph_peak_caller Goto Github PK

$ graph_peak_caller peaks_to_linear 01_max_paths.intervalcollection index/01_linear_pathv2.interval 01 01_linear_peaks.bed
2023-05-11 20:01:29,104, INFO: Converting peak 0
Traceback (most recent call last):
  File "/share/home/miniconda3/bin/graph_peak_caller", line 33, in <module>
    sys.exit(load_entry_point('graph-peak-caller', 'console_scripts', 'graph_peak_caller')())
  File "/share/home/software/graph_peak_caller/graph_peak_caller/command_line_interface.py", line 39, in main
    run_argument_parser(sys.argv[1:])
  File "/share/home/software/graph_peak_caller/graph_peak_caller/command_line_interface.py", line 679, in run_argument_parser
    args.func(args)
  File "/share/home/software/graph_peak_caller/graph_peak_caller/analysis/analysis_interface.py", line 384, in peaks_to_linear
    linear_peaks = peaks.to_approx_linear_peaks(linear_path, args.chromosome)
  File "/share/home/software/graph_peak_caller/graph_peak_caller/peakcollection.py", line 249, in to_approx_linear_peaks
    linear_peaks.append(peak.to_approx_linear_peak(linear_path, chromosome))
  File "/share/home/software/graph_peak_caller/graph_peak_caller/peakcollection.py", line 73, in to_approx_linear_peak
    first_node = intersecting_nodes[0]
IndexError: list index out of range

DEBUG:matplotlib:$HOME=/home/fieldp
DEBUG:matplotlib:CONFIGDIR=/home/fieldp/.config/matplotlib
DEBUG:matplotlib:matplotlib data path: /home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/matplotlib/mpl-data
DEBUG:matplotlib:loaded rc file /home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc
DEBUG:matplotlib:matplotlib version 3.0.0
DEBUG:matplotlib:interactive is False
DEBUG:matplotlib:platform is linux
DEBUG:matplotlib:loaded modules: ['scipy.ndimage._ni_label', 'graph_peak_caller.logging_config', 'scipy.integrate._quad_vec', '_stat', 'builtins', 'graph_peak_caller.multiplegraphscallpeaks', 'ctypes._endian', 'concurrent.futures._base', 'scipy.version', 'email', 'asyncio.base_events', 'json', 'types', 'numpy.lib.arrayterator', 'numpy.core.getlimits', 'typing.re', 'zlib', 'scipy.sparse.linalg.eigen.lobpcg', 'scipy.optimize._spectral', 'Bio.SeqIO.PirIO', 'scipy.optimize._differentialevolution', 'scipy.integrate._quadpack', 'scipy.sparse.linalg.eigen.arpack._arpack', 'scipy.sparse.csc', 'ctypes', 'graph_peak_caller.peakcollection', 'scipy.linalg.linalg_version', 'scipy.linalg.cython_blas', 'scipy.linalg._fblas', 'scipy.sparse.extract', '_compression', 'matplotlib.cbook.deprecation', '_codecs', 'numpy.matrixlib', 'numpy.random._common', 'asyncio.streams', 'heapq', 'graph_peak_caller.linear_filter', 'inspect', 'scipy.integrate.quadrature', 'scipy.spatial.qhull', 'google.protobuf.internal.encoder', 'pyparsing', 'async_generator._util', 'matplotlib._color_data', 'scipy.linalg._procrustes', 'graph_peak_caller.control.linearintervals', 'numpy.lib.stride_tricks', '_frozen_importlib', 'scipy.interpolate._bsplines', 'google.protobuf.internal.enum_type_wrapper', 'scipy.fft._pocketfft.helper', 'signal', '_warnings', 'stream.release', 'graph_peak_caller.shiftestimation', 'graph_peak_caller.reporter', 'offsetbasedgraph.indexedinterval', 'graph_peak_caller.custom_exceptions', 'offsetbasedgraph.vcfmap', 'numpy.core._dtype', 'numpy.core.shape_base', 'scipy.sparse.csr', 'scipy.linalg._solve_toeplitz', 'numpy.lib.function_base', 'six.moves', 'sre_compile', 'scipy.fft._helper', 'scipy.optimize._lsq.bvls', 'numpy.version', 'xml.sax.saxutils', 'Bio.GenBank.Scanner', '_elementtree', 'numpy.random._bounded_integers', 'scipy.integrate._ode', 'scipy.optimize.slsqp', 'google.protobuf.descriptor_pb2', 'struct', 'xml.dom.minidom', 'xml.sax._exceptions', 'scipy.special._logsumexp', 'numpy.lib.npyio', 'google.protobuf.internal', '_multiprocessing', 'scipy.optimize._lsq.dogbox', 'scipy.sparse.linalg.eigen.lobpcg.lobpcg', 'scipy.optimize._differentiable_functions', 'unittest.suite', 'warnings', 'numpy.random._pickle', 'xml.etree.cElementTree', 'functools', 'pyexpat.errors', 'urllib.response', 'scipy.optimize.nonlin', 'scipy.interpolate', 'mpl_toolkits', 'scipy.special._ellip_harm_2', 'posixpath', 'google.protobuf.internal.python_message', 'asyncio.log', 'numpy.linalg.lapack_lite', 'numpy.polynomial.hermite', 'scipy.spatial._voronoi', 'scipy.spatial.distance', '_random', 'scipy.integrate._ivp.ivp', 'scipy.interpolate.rbf', 'scipy.interpolate._cubic', 'numpy.ma', 'scipy.optimize.linesearch', 'asyncio.tasks', 'typing.io', '_functools', 'numpy.random._mt19937', 'asyncio.subprocess', 'scipy.fft', 'scipy.sparse.linalg.eigen', 'async_generator', 'scipy.integrate._ivp.lsoda', 'email.feedparser', 'scipy.optimize.zeros', '_hashlib', 'xml.etree.ElementPath', 'scipy.ndimage.measurements', 'scipy.spatial._hausdorff', 'scipy.spatial._plotutils', 'stat', '_cython_0_29_19', 'numpy.polynomial.chebyshev', 'pwd', 'graph_peak_caller.callpeaks', 'scipy.linalg._decomp_polar', 'offsetbasedgraph', 'scipy.optimize._minimize', 'shutil', '_posixsubprocess', 'numpy.core.records', 'scipy.spatial.transform.rotation', 'scipy.sparse.linalg.isolve', 'numpy.core._methods', 'scipy.sparse.bsr', 'scipy.optimize._remove_redundancy', 'numpy.core.numerictypes', 'email.encoders', 'ntpath', 'scipy._lib._uarray._backend', 'scipy.sparse.linalg.interface', 'Bio.SeqIO.IgIO', 'scipy.optimize._trlib', '_ni_label', 'token', 'graph_peak_caller.postprocess', 'scipy.optimize._linprog_util', 'numpy.random._generator', 'xml.dom.xmlbuilder', 'scipy._lib.messagestream', 'email._parseaddr', '_collections_abc', 'scipy.sparse.csgraph._matching', 'scipy.optimize._shgo', 'scipy.integrate._ivp.dop853_coefficients', 'google.protobuf.internal.decoder', 'numpy.lib.shape_base', 'google.protobuf.descriptor', 'scipy._lib.doccer', 'numpy.testing._private.utils', '_bz2', 'scipy.spatial._spherical_voronoi', 'scipy.special._ufuncs_cxx', 'numpy.polynomial.polyutils', 'pyvg.conversion', 'Bio.SeqIO.GckIO', 'stream', 'email.iterators', 'scipy.optimize._trustregion_constr.canonical_constraint', 're', 'scipy.sparse.linalg.isolve.lgmres', 'asyncio.protocols', '_weakrefset', 'scipy.constants', 'numpy.core._add_newdocs', 'scipy.optimize._trustregion_constr.qp_subproblem', 'numpy._pytesttester', 'scipy.special.orthogonal', 'scipy._lib._threadsafety', 'scipy.optimize.optimize', 'Bio.SeqIO.SnapGeneIO', 'xml.dom.domreg', 'scipy.integrate._ivp.common', 'scipy.fft._pocketfft.realtransforms', 'scipy.optimize._trustregion_constr', 'numpy.core.memmap', 'scipy.optimize._lsq.trf', '_bisect', 'scipy._lib.uarray', 'scipy.stats._distn_infrastructure', 'http.client', 'sre_parse', 'scipy.integrate._bvp', 'cycler', 'scipy.sparse.csgraph._flow', 'encodings.latin_1', 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'_sysconfigdata', 'scipy.spatial._distance_wrap', 'xml', 'scipy.sparse.compressed', 'google.protobuf.internal.extension_dict', 'os.path', 'scipy.interpolate.dfitpack', 'scipy.spatial', 'graph_peak_caller.callpeaks_interface', '_decimal', 'binascii', '_sqlite3', 'stream.stream', 'numpy.compat.py3k', 'scipy.ndimage.filters', 'dateutil', 'multiprocessing.process', 'email.header', '_ssl', 'scipy.sparse._index', 'asyncio.compat', 'scipy.integrate', '__main__', 'scipy.optimize._dual_annealing', 'scipy.optimize._bglu_dense', 'numpy.lib.mixins', 'numpy.polynomial', '_struct', 'numpy._globals', 'Bio.Data.IUPACData', 'operator', 'graph_peak_caller.analysis.venn_diagrams', 'scipy.__config__', 'scipy.special.sf_error']
DEBUG:matplotlib:CACHEDIR=/home/fieldp/.cache/matplotlib
DEBUG:matplotlib.font_manager:Using fontManager instance from /home/fieldp/.cache/matplotlib/fontlist-v300.json
DEBUG:matplotlib.pyplot:Loaded backend agg version unknown.
2023-02-09 11:49:16,960, INFO: Sample files: ['alignments.json']
2023-02-09 11:49:16,960, INFO: Using graphs: ['ch19.nobg']
2023-02-09 11:49:16,960, INFO: Will use sequence graphs. ['ch19.nobg.sequences']
2023-02-09 11:49:16,960, INFO: Using graphs from data directory ./
2023-02-09 11:49:16,960, INFO: Will use [''] as extra experiments names for each run, based on graph file names.If only running on single graph, this should be empty.
2023-02-09 11:49:16,960, WARNING: Did not find linear map for  for graph ch19.nobg. Will create.
2023-02-09 11:49:16,960, WARNING: Did not find linear map for  for graph ch19.nobg. Will create.
2023-02-09 11:49:17,422, INFO: Getting topologically sorted nodes
2023-02-09 11:49:17,422, INFO: 0 nodes processed
Traceback (most recent call last):
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/bin/graph_peak_caller", line 8, in <module>
    sys.exit(main())
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/graph_peak_caller/command_line_interface.py", line 36, in main
    run_argument_parser(sys.argv[1:])
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/graph_peak_caller/command_line_interface.py", line 673, in run_argument_parser
    args.func(args)
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/graph_peak_caller/callpeaks_interface.py", line 182, in run_callpeaks2
    create_linear_map(graph, linear_map_name)
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/graph_peak_caller/util.py", line 6, in create_linear_map
    linear_map = LinearMap.from_graph(ob_graph)
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/graph_peak_caller/control/linearmap.py", line 104, in from_graph
    node_ids = list(graph.get_topological_sorted_node_ids())
  File "/home/fieldp/miniconda3/envs/graph_peak_caller/lib/python3.5/site-packages/offsetbasedgraph/graph.py", line 539, in get_topological_sorted_node_ids
    assert not unfinished, unfinished
AssertionError: {190627: 1}

2021-01-28 01:43:03,592, INFO: Setting sequences using vg json graph graph_p.json
Traceback (most recent call last):
  File "graph_peak_caller", line 8, in <module>
    sys.exit(main())
  File "graph_peak_caller/command_line_interface.py", line 36, in main
    run_argument_parser(sys.argv[1:])
  File "graph_peak_caller/command_line_interface.py", line 673, in run_argument_parser
    args.func(args)
  File "graph_peak_caller/preprocess_interface.py", line 67, in create_ob_graph
    sequence_graph.set_sequences_using_vg_json_graph(args.vg_json_file_name)
  File "offsetbasedgraph/sequencegraph.py", line 71, in set_sequences_using_vg_json_graph
    self.set_sequence(int(node_object["id"]), node_object["sequence"])
  File "offsetbasedgraph/sequencegraph.py", line 94, in set_sequence
    assert node_size == len(sequence), "Invalid sequence. Does not cover whole node"
AssertionError: Invalid sequence. Does not cover whole node

INFO:root:Using sequencegraph graphs/chr20.nobg.sequences
2020-10-25 19:16:51,355, INFO: Getting topologically sorted nodes
2020-10-25 19:16:51,356, INFO: 0 nodes processed
2020-10-25 19:16:51,356, INFO: Finding starts and ends
2020-10-25 19:16:51,357, INFO: 0 nodes processed
Traceback (most recent call last):
  File "/home/cgroza/.local/bin/graph_peak_caller", line 11, in <module>
    sys.exit(main())
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/command_line_interface.py", line 36, in main
    run_argument_parser(sys.argv[1:])
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/command_line_interface.py", line 673, in run_argument_parser
    args.func(args)
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/preprocess_interface.py", line 79, in create_linear_map_interface
    create_linear_map(graph, out_name)
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/util.py", line 6, in create_linear_map
    linear_map = LinearMap.from_graph(ob_graph)
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/control/linearmap.py", line 107, in from_graph
    starts = cls.find_starts(graph, node_ids)
  File "/home/cgroza/.local/lib/python3.7/site-packages/graph_peak_caller/control/linearmap.py", line 137, in find_starts
    max_dists[j] = max(cur_dist, max_dists[j])
IndexError: index -246491878 is out of bounds for axis 0 with size 2