/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/xphyle-4.2.2-py3.6.egg/xphyle/paths.py:149: DeprecationWarning: Use of resolve_path with string path arguments is deprected (lineno /hpc/local/CentOS7/common/lang/python/3.6.1/lib/python3.6/argparse.py:2261)
  f"Use of {func.__name__} with string path arguments is "
2020-05-07 10:55:57.469 | INFO     | atropos.commands.console:_setup_logging:247 - This is Atropos 2.0.0a5 with Python 3.6.1
%(asctime)s %(levelname)s: %(message)s
2020-05-07 10:55:57.484 | ERROR    | atropos.console:execute_cli:151 - Error executing command: trim
Traceback (most recent call last):
  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/bin/atropos", line 11, in <module>
    load_entry_point('atropos==2.0.0a5', 'console_scripts', 'atropos')()
    -> <function load_entry_point at 0x2b8d67f6b268>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/__main__.py", line 17, in main
    sys.exit(run_atropos(args))
    |   |    |           -> None
    |   |    -> <function run_atropos at 0x2b8d63428268>
    |   -> <built-in function exit>
    -> <module 'sys' (built-in)>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/console.py", line 56, in run_atropos
    return execute_cli(args)
           |           -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '-se', 'TM433_trunc.bam', '--input-format', 'bam', '-o', 'testout.sam', '--output-fo...
           -> <function execute_cli at 0x2b8d6a14a9d8>

> File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/console.py", line 144, in execute_cli
    retcode, summary = command.execute(args)
                       |       |       -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '-se', 'TM433_trunc.bam', '--input-format', 'bam', '-o', 'testout.sam', '--output-fo...
                       |       -> <classmethod object at 0x2b8d6a142b70>
                       -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 143, in execute
    command = cls._create_command(options)
              |   |               -> Namespace(accession=None, action=<TrimAction.TRIM: 'trim'>, adapter_cache_file=PosixPath('/home/gen/philip/proj/atropos/.adap...
              |   -> <classmethod object at 0x2b8d6a142be0>
              -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 177, in _create_command
    return cast(Type[BaseCommand], cls)(options)
           |    |    |             |    -> Namespace(accession=None, action=<TrimAction.TRIM: 'trim'>, adapter_cache_file=PosixPath('/home/gen/philip/proj/atropos/.adap...
           |    |    |             -> atropos.commands.trim.console.TrimCommandConsole
           |    |    -> atropos.commands.BaseCommand
           |    -> typing.Type
           -> <function cast at 0x2b8d67ffe378>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 175, in __init__
    self.reader = reader = open_reader(**open_args)
    |                      |             -> {'file_format': <SequenceFileType.BAM: ({'.bam'}, False)>, 'quality_base': 33, 'colorspace': False, 'input_read': <InputRead....
    |                      -> <function open_reader at 0x2b8d6a0bf620>
    -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b8d6a4b04a8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 1136, in open_reader
    file1, quality_base=quality_base, alphabet=alphabet
    |                   |                      -> None
    |                   -> 33
    -> PosixPath('/home/gen/philip/proj/atropos/TM433_trunc.bam')

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 815, in __init__
    self._parser = BAMParser(self._file, **bam_kwargs)
    |              |         |    |        -> {'check_sq': False}
    |              |         |    -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |              |         -> <atropos.io.readers._impl.SingleEndSAMReader object at 0x2b8d6a4b0240>
    |              -> atropos.io.readers._impl.BAMParser
    -> <atropos.io.readers._impl.SingleEndSAMReader object at 0x2b8d6a4b0240>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 733, in __init__
    self._reader = self._load_bam_module().AlignmentFile(bam_file.name, **kwargs)
    |              |    |                                |        |       -> {'check_sq': False}
    |              |    |                                |        -> <attribute 'name' of '_io.BufferedReader' objects>
    |              |    |                                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |              |    -> <staticmethod object at 0x2b8d6a0bed30>
    |              -> <atropos.io.readers._impl.BAMParser object at 0x2b8d6a4b0048>
    -> <atropos.io.readers._impl.BAMParser object at 0x2b8d6a4b0048>

  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/core.py", line 172, in __init__
    bam.BamReader.__init__(self, **rargs)
    |   |         |        |       -> {'filepath_or_object': '/home/gen/philip/proj/atropos/TM433_trunc.bam', 'mode': 'rb', 'max_cache': 128, 'index_filename': Non...
    |   |         |        -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
    |   |         -> <function BamReader.__init__ at 0x2b8d6a577e18>
    |   -> <class 'bamnostic.bam.BamReader'>
    -> <module 'bamnostic.bam' from '/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bam.py'>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bam.py", line 239, in __init__
    super(BamReader, self).__init__(**super_args)
          |          |                -> {'filepath_or_object': '/home/gen/philip/proj/atropos/TM433_trunc.bam', 'mode': 'rb', 'max_cache': 128, 'filename': None, 'ig...
          |          -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
          -> <class 'bamnostic.bam.BamReader'>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 287, in __init__
    self._load_block(handle.tell())
    |    |           |      -> <method 'tell' of '_io.BufferedReader' objects>
    |    |           -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |    -> <function BgzfReader._load_block at 0x2b8d6a554bf8>
    -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 321, in _load_block
    block_size, self._buffer = _load_bgzf_block(handle)
                |              |                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
                |              -> <function _load_bgzf_block at 0x2b8d6a554a60>
                -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 213, in _load_bgzf_block
    header, _ = _bgzf_metaheader(handle)
                |                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
                -> <function _bgzf_metaheader at 0x2b8d6a554950>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 130, in _bgzf_metaheader
    raise ValueError('Malformed BGZF block')

ValueError: Malformed BGZF block
%(asctime)s %(levelname)s: %(message)s
Traceback (most recent call last):
  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/bin/atropos", line 11, in <module>
    load_entry_point('atropos==2.0.0a5', 'console_scripts', 'atropos')()
    -> <function load_entry_point at 0x2b8d67f6b268>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/__main__.py", line 17, in main
    sys.exit(run_atropos(args))
    |   |    |           -> None
    |   |    -> <function run_atropos at 0x2b8d63428268>
    |   -> <built-in function exit>
    -> <module 'sys' (built-in)>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/console.py", line 56, in run_atropos
    return execute_cli(args)
           |           -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '-se', 'TM433_trunc.bam', '--input-format', 'bam', '-o', 'testout.sam', '--output-fo...
           -> <function execute_cli at 0x2b8d6a14a9d8>

> File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/console.py", line 144, in execute_cli
    retcode, summary = command.execute(args)
                       |       |       -> ['-a', 'RA5=GATCGTCGGACTGTAGAACTCTGAAC', '-se', 'TM433_trunc.bam', '--input-format', 'bam', '-o', 'testout.sam', '--output-fo...
                       |       -> <classmethod object at 0x2b8d6a142b70>
                       -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 143, in execute
    command = cls._create_command(options)
              |   |               -> Namespace(accession=None, action=<TrimAction.TRIM: 'trim'>, adapter_cache_file=PosixPath('/home/gen/philip/proj/atropos/.adap...
              |   -> <classmethod object at 0x2b8d6a142be0>
              -> atropos.commands.trim.console.TrimCommandConsole

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/console.py", line 177, in _create_command
    return cast(Type[BaseCommand], cls)(options)
           |    |    |             |    -> Namespace(accession=None, action=<TrimAction.TRIM: 'trim'>, adapter_cache_file=PosixPath('/home/gen/philip/proj/atropos/.adap...
           |    |    |             -> atropos.commands.trim.console.TrimCommandConsole
           |    |    -> atropos.commands.BaseCommand
           |    -> typing.Type
           -> <function cast at 0x2b8d67ffe378>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 175, in __init__
    self.reader = reader = open_reader(**open_args)
    |                      |             -> {'file_format': <SequenceFileType.BAM: ({'.bam'}, False)>, 'quality_base': 33, 'colorspace': False, 'input_read': <InputRead....
    |                      -> <function open_reader at 0x2b8d6a0bf620>
    -> <atropos.commands.trim.console.TrimCommandConsole object at 0x2b8d6a4b04a8>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 1136, in open_reader
    file1, quality_base=quality_base, alphabet=alphabet
    |                   |                      -> None
    |                   -> 33
    -> PosixPath('/home/gen/philip/proj/atropos/TM433_trunc.bam')

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 815, in __init__
    self._parser = BAMParser(self._file, **bam_kwargs)
    |              |         |    |        -> {'check_sq': False}
    |              |         |    -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |              |         -> <atropos.io.readers._impl.SingleEndSAMReader object at 0x2b8d6a4b0240>
    |              -> atropos.io.readers._impl.BAMParser
    -> <atropos.io.readers._impl.SingleEndSAMReader object at 0x2b8d6a4b0240>

  File "/hpc/local/CentOS7/gen/software/atropos-2.0.0-alpha.5/lib/python3.6/site-packages/atropos-2.0.0a5-py3.6-linux-x86_64.egg/atropos/io/readers/_impl.py", line 733, in __init__
    self._reader = self._load_bam_module().AlignmentFile(bam_file.name, **kwargs)
    |              |    |                                |        |       -> {'check_sq': False}
    |              |    |                                |        -> <attribute 'name' of '_io.BufferedReader' objects>
    |              |    |                                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |              |    -> <staticmethod object at 0x2b8d6a0bed30>
    |              -> <atropos.io.readers._impl.BAMParser object at 0x2b8d6a4b0048>
    -> <atropos.io.readers._impl.BAMParser object at 0x2b8d6a4b0048>

  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/core.py", line 172, in __init__
    bam.BamReader.__init__(self, **rargs)
    |   |         |        |       -> {'filepath_or_object': '/home/gen/philip/proj/atropos/TM433_trunc.bam', 'mode': 'rb', 'max_cache': 128, 'index_filename': Non...
    |   |         |        -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
    |   |         -> <function BamReader.__init__ at 0x2b8d6a577e18>
    |   -> <class 'bamnostic.bam.BamReader'>
    -> <module 'bamnostic.bam' from '/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bam.py'>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bam.py", line 239, in __init__
    super(BamReader, self).__init__(**super_args)
          |          |                -> {'filepath_or_object': '/home/gen/philip/proj/atropos/TM433_trunc.bam', 'mode': 'rb', 'max_cache': 128, 'filename': None, 'ig...
          |          -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
          -> <class 'bamnostic.bam.BamReader'>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 287, in __init__
    self._load_block(handle.tell())
    |    |           |      -> <method 'tell' of '_io.BufferedReader' objects>
    |    |           -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
    |    -> <function BgzfReader._load_block at 0x2b8d6a554bf8>
    -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 321, in _load_block
    block_size, self._buffer = _load_bgzf_block(handle)
                |              |                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
                |              -> <function _load_bgzf_block at 0x2b8d6a554a60>
                -> <bamnostic.core.AlignmentFile object at 0x2b8d6a4b0e48>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 213, in _load_bgzf_block
    header, _ = _bgzf_metaheader(handle)
                |                -> <_io.BufferedReader name='/home/gen/philip/proj/atropos/TM433_trunc.bam'>
                -> <function _bgzf_metaheader at 0x2b8d6a554950>
  File "/hpc/local/CentOS7/gen/lib/python3.6/site-packages/bamnostic/bgzf.py", line 130, in _bgzf_metaheader
    raise ValueError('Malformed BGZF block')

ValueError: Malformed BGZF block